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PDBsum entry 1bu7

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1bu7
Jmol
Contents
Protein chains
455 a.a. *
Ligands
HEM ×2
EDO ×14
Waters ×998
* Residue conservation analysis
PDB id:
1bu7
Name: Oxidoreductase
Title: Cryogenic structure of cytochrome p450bm-3 heme domain
Structure: Protein (cytochrome p450). Chain: a, b. Fragment: heme domain. Synonym: fatty acid hydroxylase. Engineered: yes
Source: Bacillus megaterium. Organism_taxid: 1404. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21(de3). Other_details: synthetic gene
Resolution:
1.65Å     R-factor:   0.197     R-free:   0.251
Authors: H.Li,T.L.Poulos
Key ref:
I.F.Sevrioukova et al. (1999). Structure of a cytochrome P450-redox partner electron-transfer complex. Proc Natl Acad Sci U S A, 96, 1863-1868. PubMed id: 10051560 DOI: 10.1073/pnas.96.5.1863
Date:
14-Sep-98     Release date:   23-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P14779  (CPXB_BACME) -  Bifunctional P-450/NADPH-P450 reductase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1049 a.a.
455 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.14.14.1  - Unspecific monooxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RH + reduced flavoprotein + O2 = ROH + oxidized flavoprotein + H2O
RH
+ reduced flavoprotein
+ O(2)
= ROH
+ oxidized flavoprotein
+ H(2)O
      Cofactor: Heme-thiolate
   Enzyme class 3: E.C.1.6.2.4  - NADPH--hemoprotein reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADPH + n oxidized hemoprotein = NADP+ + n reduced hemoprotein
NADPH
+ n oxidized hemoprotein
= NADP(+)
+ n reduced hemoprotein
      Cofactor: FAD; FMN
FAD
FMN
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen     3 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.96.5.1863 Proc Natl Acad Sci U S A 96:1863-1868 (1999)
PubMed id: 10051560  
 
 
Structure of a cytochrome P450-redox partner electron-transfer complex.
I.F.Sevrioukova, H.Li, H.Zhang, J.A.Peterson, T.L.Poulos.
 
  ABSTRACT  
 
The crystal structure of the complex between the heme- and FMN-binding domains of bacterial cytochrome P450BM-3, a prototype for the complex between eukaryotic microsomal P450s and P450 reductase, has been determined at 2.03 A resolution. The flavodoxin-like flavin domain is positioned at the proximal face of the heme domain with the FMN 4.0 and 18.4 A from the peptide that precedes the heme-binding loop and the heme iron, respectively. The heme-binding peptide represents the most efficient and coupled through-bond electron pathway to the heme iron. Substantial differences between the FMN-binding domains of P450BM-3 and microsomal P450 reductase, observed around the flavin-binding sites, are responsible for different redox properties of the FMN, which, in turn, control electron flow to the P450.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. The heme-FMN domain interface. Blue and yellow colors are assigned to the backbones for the heme and flavin domains, respectively. Some of the solvent molecules mediating domain-domain interaction are shown in red. The dotted lines represent hydrogen bonds and salt bridges. The Pro-382-Cys-400 part of the heme-binding peptide provides a direct through-bond electron transfer pathway from the FMN to the heme.
Figure 3.
Fig. 3. Electrostatic potential at the molecular surfaces in the interface between the heme and FMN domains of P450BM-3 (A) and around the flavin-binding site of the FMN domain of P450BM-3 and its structural and functional analogs (B). The diagrams were prepared with GRASP (57). The deepest shades of blue and red correspond to potentials of +16 kT and 16 kT, respectively, whereas neutral points are colored white. The surfaces were made semitransparent to show cofactors and residues involved in the interaction. (A) To display the interacting surfaces between the heme and FMN domains of P450BM-3, the latter has been detached and rotated by 180°. (B) The proteins shown are (a) FMN domain of P450BM-3, (b) D. vulgaris flavodoxin (29), and (c) FMN domain of microsomal P450 reductase (16). All three are oriented approximately the same with the FMN-binding site facing the viewer.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
20125119 B.B.Palma, M.S.E Sousa, C.R.Vosmeer, J.Lastdrager, J.Rueff, N.P.Vermeulen, and M.Kranendonk (2010).
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21110374 C.J.Whitehouse, W.Yang, J.A.Yorke, B.C.Rowlatt, A.J.Strong, C.F.Blanford, S.G.Bell, M.Bartlam, L.L.Wong, and Z.Rao (2010).
Structural basis for the properties of two single-site proline mutants of CYP102A1 (P450BM3).
  Chembiochem, 11, 2549-2556.
PDB code: 3m4v
20387782 D.Fishelovitch, S.Shaik, H.J.Wolfson, and R.Nussinov (2010).
How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?
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19808095 D.Ghosh, J.Griswold, M.Erman, and W.Pangborn (2010).
X-ray structure of human aromatase reveals an androgen-specific active site.
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20026040 D.R.Davydov, E.V.Sineva, S.Sistla, N.Y.Davydova, D.J.Frank, S.G.Sligar, and J.R.Halpert (2010).
Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium.
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20180779 H.M.Girvan, C.W.Levy, P.Williams, K.Fisher, M.R.Cheesman, S.E.Rigby, D.Leys, and A.W.Munro (2010).
Glutamate-haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3.
  Biochem J, 427, 455-466.
PDB codes: 3kx3 3kx4 3kx5
  21048857 I.Axarli, A.Prigipaki, and N.E.Labrou (2010).
Cytochrome P450 102A2 Catalyzes Efficient Oxidation of Sodium Dodecyl Sulphate: A Molecular Tool for Remediation.
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20446763 T.C.Pochapsky, S.Kazanis, and M.Dang (2010).
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19944754 Y.Hong, H.Li, Y.C.Yuan, and S.Chen (2010).
Sequence-function correlation of aromatase and its interaction with reductase.
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19865780 C.S.Porro, D.Kumar, and S.P.de Visser (2009).
Electronic properties of pentacoordinated heme complexes in cytochrome P450 enzymes: search for an Fe(i) oxidation state.
  Phys Chem Chem Phys, 11, 10219-10226.  
19171935 D.Hamdane, C.Xia, S.C.Im, H.Zhang, J.J.Kim, and L.Waskell (2009).
Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450.
  J Biol Chem, 284, 11374-11384.
PDB code: 3es9
19858215 J.Ellis, A.Gutierrez, I.L.Barsukov, W.C.Huang, J.G.Grossmann, and G.C.Roberts (2009).
Domain motion in cytochrome P450 reductase: conformational equilibria revealed by NMR and small-angle x-ray scattering.
  J Biol Chem, 284, 36628-36637.  
19483672 L.Aigrain, D.Pompon, S.Moréra, and G.Truan (2009).
Structure of the open conformation of a functional chimeric NADPH cytochrome P450 reductase.
  EMBO Rep, 10, 742-747.
PDB code: 3fjo
19432415 M.Kasim, H.C.Chen, and R.P.Swenson (2009).
Functional characterization of the re-face loop spanning residues 536-541 and its interactions with the cofactor in the flavin mononucleotide-binding domain of flavocytochrome P450 from Bacillus megaterium.
  Biochemistry, 48, 5131-5141.  
19290671 R.P.Ilagan, J.Tejero, K.S.Aulak, S.S.Ray, C.Hemann, Z.Q.Wang, M.Gangoda, J.L.Zweier, and D.J.Stuehr (2009).
Regulation of FMN subdomain interactions and function in neuronal nitric oxide synthase.
  Biochemistry, 48, 3864-3876.  
19956630 Y.Hong, H.Li, J.Ye, Y.Miki, Y.C.Yuan, H.Sasano, D.B.Evans, and S.Chen (2009).
Epitope characterization of an aromatase monoclonal antibody suitable for the assessment of intratumoral aromatase activity.
  PLoS One, 4, e8050.  
19250198 Y.Hong, H.Li, Y.C.Yuan, and S.Chen (2009).
Molecular characterization of aromatase.
  Ann N Y Acad Sci, 1155, 112-120.  
17964298 B.L.Hilker, H.Fukushige, C.Hou, and D.Hildebrand (2008).
Comparison of Bacillus monooxygenase genes for unique fatty acid production.
  Prog Lipid Res, 47, 1.  
18980384 C.G.Gherasim, U.Zaman, A.Raza, and R.Banerjee (2008).
Impeded electron transfer from a pathogenic FMN domain mutant of methionine synthase reductase and its responsiveness to flavin supplementation.
  Biochemistry, 47, 12515-12522.  
18392864 C.K.Chen, T.K.h.Shokhireva, R.E.Berry, H.Zhang, and F.A.Walker (2008).
The effect of mutation of F87 on the properties of CYP102A1-CYP4C7 chimeras: altered regiospecificity and substrate selectivity.
  J Biol Inorg Chem, 13, 813-824.  
17957765 E.Stjernschantz, B.M.van Vugt-Lussenburg, A.Bonifacio, S.B.de Beer, G.van der Zwan, C.Gooijer, J.N.Commandeur, N.P.Vermeulen, and C.Oostenbrink (2008).
Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3.
  Proteins, 71, 336-352.  
18852262 H.Li, A.Das, H.Sibhatu, J.Jamal, S.G.Sligar, and T.L.Poulos (2008).
Exploring the electron transfer properties of neuronal nitric-oxide synthase by reversal of the FMN redox potential.
  J Biol Chem, 283, 34762-34772.  
18415984 H.M.Li, L.H.Mei, V.B.Urlacher, and R.D.Schmid (2008).
Cytochrome P450 BM-3 evolved by random and saturation mutagenesis as an effective indole-hydroxylating catalyst.
  Appl Biochem Biotechnol, 144, 27-36.  
18473391 R.J.Branco, A.Seifert, M.Budde, V.B.Urlacher, M.J.Ramos, and J.Pleiss (2008).
Anchoring effects in a wide binding pocket: the molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium.
  Proteins, 73, 597-607.  
17318599 A.Bonifacio, A.R.Groenhof, P.H.Keizers, C.de Graaf, J.N.Commandeur, N.P.Vermeulen, A.W.Ehlers, K.Lammertsma, C.Gooijer, and G.van der Zwan (2007).
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.
  J Biol Inorg Chem, 12, 645-654.  
17534532 A.W.Munro, H.M.Girvan, and K.J.McLean (2007).
Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily.
  Nat Prod Rep, 24, 585-609.  
17905887 E.Leonard, and M.A.Koffas (2007).
Engineering of artificial plant cytochrome P450 enzymes for synthesis of isoflavones by Escherichia coli.
  Appl Environ Microbiol, 73, 7246-7251.  
17174478 J.J.Perry, L.Fan, and J.A.Tainer (2007).
Developing master keys to brain pathology, cancer and aging from the structural biology of proteins controlling reactive oxygen species and DNA repair.
  Neuroscience, 145, 1280-1299.  
17322527 K.A.Feenstra, E.B.Starikov, V.B.Urlacher, J.N.Commandeur, and N.P.Vermeulen (2007).
Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants.
  Protein Sci, 16, 420-431.  
17379142 M.Landwehr, M.Carbone, C.R.Otey, Y.Li, and F.H.Arnold (2007).
Diversification of catalytic function in a synthetic family of chimeric cytochrome p450s.
  Chem Biol, 14, 269-278.  
17223703 R.C.Bruckner, G.Zhao, P.Ferreira, and M.S.Jorns (2007).
A mobile tryptophan is the intrinsic charge transfer donor in a flavoenzyme essential for nikkomycin antibiotic biosynthesis.
  Biochemistry, 46, 819-827.  
16915000 C.E.Flück, and W.L.Miller (2006).
P450 oxidoreductase deficiency: a new form of congenital adrenal hyperplasia.
  Curr Opin Pediatr, 18, 435-441.  
17020766 C.W.Chiang, H.C.Yeh, L.H.Wang, and N.L.Chan (2006).
Crystal structure of the human prostacyclin synthase.
  J Mol Biol, 364, 266-274.
PDB code: 2iag
16862534 D.Roccatano, T.S.Wong, U.Schwaneberg, and M.Zacharias (2006).
Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study.
  Biopolymers, 83, 467-476.  
16477023 H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, and Y.Shiro (2006).
Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.
  Proc Natl Acad Sci U S A, 103, 2611-2616.
PDB codes: 2d0t 2d0u
16521141 J.Nazor, and U.Schwaneberg (2006).
Laboratory evolution of P450 BM-3 for mediated electron transfer.
  Chembiochem, 7, 638-644.  
15726636 D.Allorge, D.Bréant, J.Harlow, J.Chowdry, J.M.Lo-Guidice, D.Chevalier, C.Cauffiez, M.Lhermitte, F.E.Blaney, G.T.Tucker, F.Broly, and S.W.Ellis (2005).
Functional analysis of CYP2D6.31 variant: homology modeling suggests possible disruption of redox partner interaction by Arg440His substitution.
  Proteins, 59, 339-346.  
15880388 D.Roccatano, T.S.Wong, U.Schwaneberg, and M.Zacharias (2005).
Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture.
  Biopolymers, 78, 259-267.  
16163453 E.Hazai, Z.Bikádi, M.Simonyi, and D.Kupfer (2005).
Association of cytochrome P450 enzymes is a determining factor in their catalytic activity.
  J Comput Aided Mol Des, 19, 271-285.  
15857787 I.Axarli, A.Prigipaki, and N.E.Labrou (2005).
Engineering the substrate specificity of cytochrome P450 CYP102A2 by directed evolution: production of an efficient enzyme for bioconversion of fine chemicals.
  Biomol Eng, 22, 81-88.  
16028060 J.Bojunga, C.Welsch, I.Antes, M.Albrecht, T.Lengauer, and S.Zeuzem (2005).
Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency.
  Hum Genet, 117, 558-564.  
15617063 J.Mestres (2005).
Structure conservation in cytochromes P450.
  Proteins, 58, 596-609.  
16283395 M.Fairhead, S.Giannini, E.M.Gillam, and G.Gilardi (2005).
Functional characterisation of an engineered multidomain human P450 2E1 by molecular Lego.
  J Biol Inorg Chem, 10, 842-853.  
16467261 W.L.Miller, N.Huang, A.V.Pandey, C.E.Flück, and V.Agrawal (2005).
P450 oxidoreductase deficiency: a new disorder of steroidogenesis.
  Ann N Y Acad Sci, 1061, 100-108.  
  16511100 Y.Ashikawa, Z.Fujimoto, H.Noguchi, H.Habe, T.Omori, H.Yamane, and H.Nojiri (2005).
Crystallization and preliminary X-ray diffraction analysis of the electron-transfer complex between the terminal oxygenase component and ferredoxin in the Rieske non-haem iron oxygenase system carbazole 1,9a-dioxygenase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 577-580.  
15071191 M.Guo, B.Bhaskar, H.Li, T.P.Barrows, and T.L.Poulos (2004).
Crystal structure and characterization of a cytochrome c peroxidase-cytochrome c site-specific cross-link.
  Proc Natl Acad Sci U S A, 101, 5940-5945.
PDB code: 1s6v
15189165 O.Pylypenko, and I.Schlichting (2004).
Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s.
  Annu Rev Biochem, 73, 991.  
12524265 A.Gorokhov, M.Negishi, E.F.Johnson, L.C.Pedersen, L.Perera, T.A.Darden, and L.G.Pedersen (2003).
Explicit water near the catalytic I helix Thr in the predicted solution structure of CYP2A4.
  Biophys J, 84, 57-68.  
14519119 B.D.Fleming, Y.Tian, S.G.Bell, L.L.Wong, V.Urlacher, and H.A.Hill (2003).
Redox properties of cytochrome p450BM3 measured by direct methods.
  Eur J Biochem, 270, 4082-4088.  
12831319 D.F.Lewis (2003).
P450 structures and oxidative metabolism of xenobiotics.
  Pharmacogenomics, 4, 387-395.  
14563924 E.E.Scott, Y.A.He, M.R.Wester, M.A.White, C.C.Chin, J.R.Halpert, E.F.Johnson, and C.D.Stout (2003).
An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution.
  Proc Natl Acad Sci U S A, 100, 13196-13201.
PDB code: 1po5
14661979 S.Izumi, H.Kaneko, T.Yamazaki, T.Hirata, and S.Kominami (2003).
Membrane topology of guinea pig cytochrome P450 17 alpha revealed by a combination of chemical modifications and mass spectrometry.
  Biochemistry, 42, 14663-14669.  
12382289 A.M.Dixon, R.M.Venable, R.W.Pastor, and T.E.Bull (2002).
Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study.
  Biopolymers, 65, 284-298.  
12076537 A.W.Munro, D.G.Leys, K.J.McLean, K.R.Marshall, T.W.Ost, S.Daff, C.S.Miles, S.K.Chapman, D.A.Lysek, C.C.Moser, C.C.Page, and P.L.Dutton (2002).
P450 BM3: the very model of a modern flavocytochrome.
  Trends Biochem Sci, 27, 250-257.  
11922954 S.B.Kirton, C.A.Baxter, and M.J.Sutcliffe (2002).
Comparative modelling of cytochromes P450.
  Adv Drug Deliv Rev, 54, 385-406.  
12211002 S.B.Kirton, C.A.Kemp, N.P.Tomkinson, S.St-Gallay, and M.J.Sutcliffe (2002).
Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6.
  Proteins, 49, 216-231.  
11997441 T.H.Bayburt, and S.G.Sligar (2002).
Single-molecule height measurements on microsomal cytochrome P450 in nanometer-scale phospholipid bilayer disks.
  Proc Natl Acad Sci U S A, 99, 6725-6730.  
12060743 T.W.Yu, L.Bai, D.Clade, D.Hoffmann, S.Toelzer, K.Q.Trinh, J.Xu, S.J.Moss, E.Leistner, and H.G.Floss (2002).
The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from Actinosynnema pretiosum.
  Proc Natl Acad Sci U S A, 99, 7968-7973.  
11493691 D.A.Hall, C.W.Vander Kooi, C.N.Stasik, S.Y.Stevens, E.R.Zuiderweg, and R.G.Matthews (2001).
Mapping the interactions between flavodoxin and its physiological partners flavodoxin reductase and cobalamin-dependent methionine synthase.
  Proc Natl Acad Sci U S A, 98, 9521-9526.  
11456500 K.R.Henne, M.B.Fisher, K.R.Iyer, D.H.Lang, W.F.Trager, and A.E.Rettie (2001).
Active site characteristics of CYP4B1 probed with aromatic ligands.
  Biochemistry, 40, 8597-8605.  
11559350 P.Hlavica, and D.F.Lewis (2001).
Allosteric phenomena in cytochrome P450-catalyzed monooxygenations.
  Eur J Biochem, 268, 4817-4832.  
  11082183 A.Daiber, S.Herold, C.Schöneich, D.Namgaladze, J.A.Peterson, and V.Ullrich (2000).
Nitration and inactivation of cytochrome P450BM-3 by peroxynitrite. Stopped-flow measurements prove ferryl intermediates.
  Eur J Biochem, 267, 6729-6739.  
10673428 B.M.Hallberg, T.Bergfors, K.Bäckbro, G.Pettersson, G.Henriksson, and C.Divne (2000).
A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase.
  Structure, 8, 79-88.
PDB codes: 1d7b 1d7c 1d7d
11150615 C.S.Miles, T.W.Ost, M.A.Noble, A.W.Munro, and S.K.Chapman (2000).
Protein engineering of cytochromes P-450.
  Biochim Biophys Acta, 1543, 383-407.  
11106776 D.F.Lewis, and P.Hlavica (2000).
Interactions between redox partners in various cytochrome P450 systems: functional and structural aspects.
  Biochim Biophys Acta, 1460, 353-374.  
10678174 P.A.Williams, J.Cosme, V.Sridhar, E.F.Johnson, and D.E.McRee (2000).
Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity.
  Mol Cell, 5, 121-131.
PDB code: 1dt6
10704198 Y.T.Chang, and G.Loew (2000).
Homology modeling, molecular dynamics simulations, and analysis of CYP119, a P450 enzyme from extreme acidothermophilic archaeon Sulfolobus solfataricus.
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10562539 B.R.Crane, R.J.Rosenfeld, A.S.Arvai, D.K.Ghosh, S.Ghosh, J.A.Tainer, D.J.Stuehr, and E.D.Getzoff (1999).
N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization.
  EMBO J, 18, 6271-6281.
PDB codes: 1df1 1qom
10570242 H.Li, and T.L.Poulos (1999).
Fatty acid metabolism, conformational change, and electron transfer in cytochrome P-450(BM-3).
  Biochim Biophys Acta, 1441, 141-149.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.