PDBsum entry 1ki1

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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
Jmol PyMol
Protein chains
178 a.a. *
342 a.a. *
SO4 ×2
Waters ×181
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Guanine nucleotide exchange region of intersectin in complex with cdc42
Structure: G25k gtp-binding protein, placental isoform. Chain: a, c. Fragment: residues 1-188. Synonym: cdc42. Engineered: yes. Mutation: yes. Intersectin long form. Chain: b, d. Fragment: dbl homology and pleckstrin homology domains
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.231     R-free:   0.247
Authors: J.T.Snyder,W.M.Pruitt,C.J.Der,J.Sondek
Key ref:
J.T.Snyder et al. (2002). Structural basis for the selective activation of Rho GTPases by Dbl exchange factors. Nat Struct Biol, 9, 468-475. PubMed id: 12006984 DOI: 10.1038/nsb796
02-Dec-01     Release date:   29-May-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P60953  (CDC42_HUMAN) -  Cell division control protein 42 homolog
191 a.a.
178 a.a.
Protein chains
Pfam   ArchSchema ?
Q15811  (ITSN1_HUMAN) -  Intersectin-1
1721 a.a.
342 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   28 terms 
  Biological process     cardiac conduction system development   84 terms 
  Biochemical function     nucleotide binding     15 terms  


DOI no: 10.1038/nsb796 Nat Struct Biol 9:468-475 (2002)
PubMed id: 12006984  
Structural basis for the selective activation of Rho GTPases by Dbl exchange factors.
J.T.Snyder, D.K.Worthylake, K.L.Rossman, L.Betts, W.M.Pruitt, D.P.Siderovski, C.J.Der, J.Sondek.
Activation of Rho-family GTPases involves the removal of bound GDP and the subsequent loading of GTP, all catalyzed by guanine nucleotide exchange factors (GEFs) of the Dbl-family. Despite high sequence conservation among Rho GTPases, Dbl proteins possess a wide spectrum of discriminatory potentials for Rho-family members. To rationalize this specificity, we have determined crystal structures of the conserved, catalytic fragments (Dbl and pleckstrin homology domains) of the exchange factors intersectin and Dbs in complex with their cognate GTPases, Cdc42 and RhoA, respectively. Structure-based mutagenesis of intersectin and Dbs reveals the key determinants responsible for promoting exchange activity in Cdc42, Rac1 and RhoA. These findings provide critical insight into the structural features necessary for the proper pairing of Dbl-exchange factors with Rho GTPases and now allow for the detailed manipulation of signaling pathways mediated by these oncoproteins in vivo.
  Selected figure(s)  
Figure 1.
Figure 1. Overall structures of ITSN -Cdc42 and Dbs -RhoA. a, Stereo view of an electron density map calculated using density-modified MAD experimental phases contoured at 1.2 and displayed with the refined 6 helix of the DH domain of ITSN. b, Stereo view of a representative portion of the 2F[o]-F[c] electron density of the Dbs -RhoA structure, contoured at 1.3 and displayed with residues 759 -772 of Dbs (yellow) and residues 54 -62 of RhoA (green). c, Ribbon diagram of the ITSN -Cdc42 structure. The DH domain is yellow, and the PH domain is blue, with defined secondary structural elements labeled in accordance with described nomenclature^8. Cdc42 is green, except for the switch regions (s1 = residues 26 -40 and s2 = residues 57 -76), which are red. d, Ribbon diagram of the Dbs -RhoA complex. Coloring and labeling are equivalent to the ITSN -Cdc42 structure. All figures were prepared using SPOCK ( or MOLSCRIPT36.
Figure 5.
Figure 5. Comparison of the Dbs -RhoA, Dbs -Cdc42 and Tiam1 -Rac1 structures. a, Interface of the DH domain of Dbs (yellow) and Cdc42 (green). b, Interface of the DH domain of Dbs and RhoA (green). c, Superposition of the backbone traces of the 4/ 5 loop of ITSN and Tiam1 on the Dbs -RhoA complex. ITSN (blue) and Tiam1 (red) backbones are semitransparent, and Dbs is yellow. d, Interface of the DH domain of Tiam1 (yellow) and Rac1 (green). Unless otherwise noted, coloring is according to the styles used in Fig. 3.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 468-475) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21685891 F.Calvo, V.Sanz-Moreno, L.Agudo-Ibáñez, F.Wallberg, E.Sahai, C.J.Marshall, and P.Crespo (2011).
RasGRF suppresses Cdc42-mediated tumour cell movement, cytoskeletal dynamics and transformation.
  Nat Cell Biol, 13, 819-826.  
20842712 C.Kintscher, S.Wuertenberger, R.Eylenstein, T.Uhlendorf, and Y.Groemping (2010).
Autoinhibition of GEF activity in Intersectin 1 is mediated by the short SH3-DH domain linker.
  Protein Sci, 19, 2164-2174.  
20018869 G.M.Gasmi-Seabrook, C.B.Marshall, M.Cheung, B.Kim, F.Wang, Y.J.Jang, T.W.Mak, V.Stambolic, and M.Ikura (2010).
Real-time NMR study of guanine nucleotide exchange and activation of RhoA by PDZ-RhoGEF.
  J Biol Chem, 285, 5137-5145.  
21156937 J.P.O'Bryan (2010).
Intersecting pathways in cell biology.
  Sci Signal, 3, re10.  
20585582 K.F.Ahmad, and W.A.Lim (2010).
The minimal autoinhibited unit of the guanine nucleotide exchange factor intersectin.
  PLoS One, 5, e11291.
PDB code: 3jv3
19880753 M.Aittaleb, C.A.Boguth, and J.J.Tesmer (2010).
Structure and function of heterotrimeric G protein-regulated Rho guanine nucleotide exchange factors.
  Mol Pharmacol, 77, 111-125.  
20345913 S.Reddy-Alla, B.Schmitt, J.Birkenfeld, V.Eulenburg, S.Dutertre, C.Böhringer, M.Götz, H.Betz, and T.Papadopoulos (2010).
PH-domain-driven targeting of collybistin but not Cdc42 activation is required for synaptic gephyrin clustering.
  Eur J Neurosci, 31, 1173-1184.  
21029865 S.S.Margolis, J.Salogiannis, D.M.Lipton, C.Mandel-Brehm, Z.P.Wills, A.R.Mardinly, L.Hu, P.L.Greer, J.B.Bikoff, H.Y.Ho, M.J.Soskis, M.Sahin, and M.E.Greenberg (2010).
EphB-mediated degradation of the RhoA GEF Ephexin5 relieves a developmental brake on excitatory synapse formation.
  Cell, 143, 442-455.  
18929667 F.Jelen, P.Lachowicz, W.Apostoluk, A.Mateja, Z.S.Derewenda, and J.Otlewski (2009).
Dissecting the thermodynamics of GAP-RhoA interactions.
  J Struct Biol, 165, 10-18.  
19622753 I.K.Klein, D.N.Predescu, T.Sharma, I.Knezevic, A.B.Malik, and S.Predescu (2009).
Intersectin-2L regulates caveola endocytosis secondary to Cdc42-mediated actin polymerization.
  J Biol Chem, 284, 25953-25961.  
19258322 S.Thomas, B.Ritter, D.Verbich, C.Sanson, L.Bourbonnière, R.A.McKinney, and P.S.McPherson (2009).
Intersectin regulates dendritic spine development and somatodendritic endocytosis but not synaptic vesicle recycling in hippocampal neurons.
  J Biol Chem, 284, 12410-12419.  
19670212 T.Cierpicki, J.Bielnicki, M.Zheng, J.Gruszczyk, M.Kasterka, M.Petoukhov, A.Zhang, E.J.Fernandez, D.I.Svergun, U.Derewenda, J.H.Bushweller, and Z.S.Derewenda (2009).
The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA.
  Protein Sci, 18, 2067-2079.  
19620963 Z.Huang, S.E.Sutton, A.J.Wallenfang, R.C.Orchard, X.Wu, Y.Feng, J.Chai, and N.M.Alto (2009).
Structural insights into host GTPase isoform selection by a family of bacterial GEF mimics.
  Nat Struct Mol Biol, 16, 853-860.
PDB code: 3gcg
18394145 A.Hlubek, K.O.Schink, M.Mahlert, B.Sandrock, and M.Bölker (2008).
Selective activation by the guanine nucleotide exchange factor Don1 is a main determinant of Cdc42 signalling specificity in Ustilago maydis.
  Mol Microbiol, 68, 615-623.  
18052936 A.Upadhyay, H.L.Wu, C.Williams, T.Field, E.E.Galyov, J.M.van den Elsen, and S.Bagby (2008).
The guanine-nucleotide-exchange factor BopE from Burkholderia pseudomallei adopts a compact version of the Salmonella SopE/SopE2 fold and undergoes a closed-to-open conformational change upon interaction with Cdc42.
  Biochem J, 411, 485-493.
PDB codes: 2jok 2jol
18838382 C.Huber, A.Mårtensson, G.M.Bokoch, D.Nemazee, and A.L.Gavin (2008).
FGD2, a CDC42-specific Exchange Factor Expressed by Antigen-presenting Cells, Localizes to Early Endosomes and Active Membrane Ruffles.
  J Biol Chem, 283, 34002-34012.  
18589439 J.E.Chrencik, A.Brooun, H.Zhang, I.I.Mathews, G.L.Hura, S.A.Foster, J.J.Perry, M.Streiff, P.Ramage, H.Widmer, G.M.Bokoch, J.A.Tainer, G.Weckbecker, and P.Kuhn (2008).
Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1.
  J Mol Biol, 380, 828-843.
PDB code: 3bji
18511940 J.Rapley, V.L.Tybulewicz, and K.Rittinger (2008).
Crucial structural role for the PH and C1 domains of the Vav1 exchange factor.
  EMBO Rep, 9, 655-661.
PDB code: 2vrw
18056264 M.A.Kwofie, and J.Skowronski (2008).
Specific Recognition of Rac2 and Cdc42 by DOCK2 and DOCK9 Guanine Nucleotide Exchange Factors.
  J Biol Chem, 283, 3088-3096.  
18537266 M.E.Yohe, K.Rossman, and J.Sondek (2008).
Role of the C-terminal SH3 domain and N-terminal tyrosine phosphorylation in regulation of Tim and related Dbl-family proteins.
  Biochemistry, 47, 6827-6839.  
18585704 M.R.Schiller, F.Ferraro, Y.Wang, X.M.Ma, C.E.McPherson, J.A.Sobota, N.I.Schiller, R.E.Mains, and B.A.Eipper (2008).
Autonomous functions for the Sec14p/spectrin-repeat region of Kalirin.
  Exp Cell Res, 314, 2674-2691.  
18393397 M.Soundararajan, A.Turnbull, O.Fedorov, C.Johansson, and D.A.Doyle (2008).
RhoB can adopt a Mg2+ free conformation prior to GEF binding.
  Proteins, 72, 498-505.  
18505730 Y.Ugolev, Y.Berdichevsky, C.Weinbaum, and E.Pick (2008).
Dissociation of Rac1(GDP).RhoGDI complexes by the cooperative action of anionic liposomes containing phosphatidylinositol 3,4,5-trisphosphate, Rac guanine nucleotide exchange factor, and GTP.
  J Biol Chem, 283, 22257-22271.  
18540023 Y.X.Qi, M.J.Qu, D.K.Long, B.Liu, Q.P.Yao, S.Chien, and Z.L.Jiang (2008).
Rho-GDP dissociation inhibitor alpha downregulated by low shear stress promotes vascular smooth muscle cell migration and apoptosis: a proteomic analysis.
  Cardiovasc Res, 80, 114-122.  
17275330 A.Brooun, S.A.Foster, J.E.Chrencik, E.Y.Chien, A.R.Kolatkar, M.Streiff, P.Ramage, H.Widmer, G.Weckbecker, and P.Kuhn (2007).
Remedial strategies in structural proteomics: expression, purification, and crystallization of the Vav1/Rac1 complex.
  Protein Expr Purif, 53, 51-62.  
17289591 G.Dong, M.Medkova, P.Novick, and K.M.Reinisch (2007).
A catalytic coiled coil: structural insights into the activation of the Rab GTPase Sec4p by Sec2p.
  Mol Cell, 25, 455-462.
PDB code: 2ocy
17214551 K.Gotthardt, and M.R.Ahmadian (2007).
Asef is a Cdc42-specific guanine nucleotide exchange factor.
  Biol Chem, 388, 67-71.  
17190834 K.Murayama, M.Shirouzu, Y.Kawasaki, M.Kato-Murayama, K.Hanawa-Suetsugu, A.Sakamoto, Y.Katsura, A.Suenaga, M.Toyama, T.Terada, M.Taiji, T.Akiyama, and S.Yokoyama (2007).
Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism.
  J Biol Chem, 282, 4238-4242.
PDB code: 2dx1
17875942 M.Das, E.Scappini, N.P.Martin, K.A.Wong, S.Dunn, Y.J.Chen, S.L.Miller, J.Domin, and J.P.O'Bryan (2007).
Regulation of neuron survival through an intersectin-phosphoinositide 3'-kinase C2beta-AKT pathway.
  Mol Cell Biol, 27, 7906-7917.  
17337446 M.E.Yohe, K.L.Rossman, O.S.Gardner, A.E.Karnoub, J.T.Snyder, S.Gershburg, L.M.Graves, C.J.Der, and J.Sondek (2007).
Auto-inhibition of the Dbl family protein Tim by an N-terminal helical motif.
  J Biol Chem, 282, 13813-13823.  
17391702 M.K.Chhatriwala, L.Betts, D.K.Worthylake, and J.Sondek (2007).
The DH and PH domains of Trio coordinately engage Rho GTPases for their efficient activation.
  J Mol Biol, 368, 1307-1320.
PDB code: 2nz8
17704816 N.Mitin, L.Betts, M.E.Yohe, C.J.Der, J.Sondek, and K.L.Rossman (2007).
Release of autoinhibition of ASEF by APC leads to CDC42 activation and tumor suppression.
  Nat Struct Mol Biol, 14, 814-823.
PDB code: 2pz1
17606614 R.J.Rojas, M.E.Yohe, S.Gershburg, T.Kawano, T.Kozasa, and J.Sondek (2007).
Galphaq directly activates p63RhoGEF and Trio via a conserved extension of the Dbl homology-associated pleckstrin homology domain.
  J Biol Chem, 282, 29201-29210.  
18096806 S.Lutz, A.Shankaranarayanan, C.Coco, M.Ridilla, M.R.Nance, C.Vettel, D.Baltus, C.R.Evelyn, R.R.Neubig, T.Wieland, and J.J.Tesmer (2007).
Structure of Galphaq-p63RhoGEF-RhoA complex reveals a pathway for the activation of RhoA by GPCRs.
  Science, 318, 1923-1927.
PDB code: 2rgn
16541104 A.Itzen, O.Pylypenko, R.S.Goody, K.Alexandrov, and A.Rak (2006).
Nucleotide exchange via local protein unfolding--structure of Rab8 in complex with MSS4.
  EMBO J, 25, 1445-1455.
PDB code: 2fu5
16954208 A.Oleksy, Ć..OpaliƄski, U.Derewenda, Z.S.Derewenda, and J.Otlewski (2006).
The molecular basis of RhoA specificity in the guanine nucleotide exchange factor PDZ-RhoGEF.
  J Biol Chem, 281, 32891-32897.  
16467373 M.Liu, and A.Horowitz (2006).
A PDZ-binding motif as a critical determinant of Rho guanine exchange factor function and cell phenotype.
  Mol Biol Cell, 17, 1880-1887.  
16644733 M.R.Schiller, K.Chakrabarti, G.F.King, N.I.Schiller, B.A.Eipper, and M.W.Maciejewski (2006).
Regulation of RhoGEF activity by intramolecular and intermolecular SH3 domain interactions.
  J Biol Chem, 281, 18774-18786.
PDB code: 1u3o
16702219 Y.Ugolev, S.Molshanski-Mor, C.Weinbaum, and E.Pick (2006).
Liposomes comprising anionic but not neutral phospholipids cause dissociation of Rac(1 or 2) x RhoGDI complexes and support amphiphile-independent NADPH oxidase activation by such complexes.
  J Biol Chem, 281, 19204-19219.  
16613852 Z.Liu, E.V.Kostenko, G.M.Mahon, O.O.Olabisi, and I.P.Whitehead (2006).
Transformation by the Rho-specific guanine nucleotide exchange factor Dbs requires ROCK I-mediated phosphorylation of myosin light chain.
  J Biol Chem, 281, 16043-16051.  
  15951850 D.P.Siderovski, and F.S.Willard (2005).
The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits.
  Int J Biol Sci, 1, 51-66.  
15513926 E.Dransart, A.Morin, J.Cherfils, and B.Olofsson (2005).
Uncoupling of inhibitory and shuttling functions of rho GDP dissociation inhibitors.
  J Biol Chem, 280, 4674-4683.  
15817389 K.L.Rossman, and J.Sondek (2005).
Larger than Dbl: new structural insights into RhoA activation.
  Trends Biochem Sci, 30, 163-165.  
15897194 R.E.Joseph, and F.A.Norris (2005).
Substrate specificity and recognition is conferred by the pleckstrin homology domain of the Dbl family guanine nucleotide exchange factor P-Rex2.
  J Biol Chem, 280, 27508-27512.  
15339665 A.Delprato, E.Merithew, and D.G.Lambright (2004).
Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5.
  Cell, 118, 607-617.
PDB code: 1txu
14999155 A.E.Karnoub, M.Symons, S.L.Campbell, and C.J.Der (2004).
Molecular basis for Rho GTPase signaling specificity.
  Breast Cancer Res Treat, 84, 61-71.  
14597635 B.Debreceni, Y.Gao, F.Guo, K.Zhu, B.Jia, and Y.Zheng (2004).
Mechanisms of guanine nucleotide exchange and Rac-mediated signaling revealed by a dominant negative trio mutant.
  J Biol Chem, 279, 3777-3786.  
15274927 D.K.Worthylake, K.L.Rossman, and J.Sondek (2004).
Crystal structure of the DH/PH fragment of Dbs without bound GTPase.
  Structure, 12, 1078-1086.
PDB code: 1rj2
14973186 J.Korlach, D.W.Baird, A.A.Heikal, K.R.Gee, G.R.Hoffman, and W.W.Webb (2004).
Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs.
  Proc Natl Acad Sci U S A, 101, 2800-2805.  
15199069 K.R.Skowronek, F.Guo, Y.Zheng, and N.Nassar (2004).
The C-terminal basic tail of RhoG assists the guanine nucleotide exchange factor trio in binding to phospholipids.
  J Biol Chem, 279, 37895-37907.
PDB code: 1nty
15306850 Q.Feng, D.Baird, and R.A.Cerione (2004).
Novel regulatory mechanisms for the Dbl family guanine nucleotide exchange factor Cool-2/alpha-Pix.
  EMBO J, 23, 3492-3504.  
15577926 R.Dvorsky, and M.R.Ahmadian (2004).
Always look on the bright site of Rho: structural implications for a conserved intermolecular interface.
  EMBO Rep, 5, 1130-1136.  
15331592 R.Kristelly, G.Gao, and J.J.Tesmer (2004).
Structural determinants of RhoA binding and nucleotide exchange in leukemia-associated Rho guanine-nucleotide exchange factor.
  J Biol Chem, 279, 47352-47362.
PDB codes: 1txd 1x86
15128949 Y.Gao, J.B.Dickerson, F.Guo, J.Zheng, and Y.Zheng (2004).
Rational design and characterization of a Rac GTPase-specific small molecule inhibitor.
  Proc Natl Acad Sci U S A, 101, 7618-7623.  
12637530 E.J.Fuentes, A.E.Karnoub, M.A.Booden, C.J.Der, and S.L.Campbell (2003).
Critical role of the pleckstrin homology domain in Dbs signaling and growth regulation.
  J Biol Chem, 278, 21188-21196.  
12657629 J.T.Snyder, A.U.Singer, M.R.Wing, T.K.Harden, and J.Sondek (2003).
The pleckstrin homology domain of phospholipase C-beta2 as an effector site for Rac.
  J Biol Chem, 278, 21099-21104.  
12637522 K.L.Rossman, L.Cheng, G.M.Mahon, R.J.Rojas, J.T.Snyder, I.P.Whitehead, and J.Sondek (2003).
Multifunctional roles for the PH domain of Dbs in regulating Rho GTPase activation.
  J Biol Chem, 278, 18393-18400.  
12471028 K.Robbe, A.Otto-Bruc, P.Chardin, and B.Antonny (2003).
Dissociation of GDP dissociation inhibitor and membrane translocation are required for efficient activation of Rac by the Dbl homology-pleckstrin homology region of Tiam.
  J Biol Chem, 278, 4756-4762.  
12525493 M.A.Baumeister, L.Martinu, K.L.Rossman, J.Sondek, M.A.Lemmon, and M.M.Chou (2003).
Loss of phosphatidylinositol 3-phosphate binding by the C-terminal Tiam-1 pleckstrin homology domain prevents in vivo Rac1 activation without affecting membrane targeting.
  J Biol Chem, 278, 11457-11464.  
14506234 M.A.Salazar, A.V.Kwiatkowski, L.Pellegrini, G.Cestra, M.H.Butler, K.L.Rossman, D.M.Serna, J.Sondek, F.B.Gertler, and P.De Camilli (2003).
Tuba, a novel protein containing bin/amphiphysin/Rvs and Dbl homology domains, links dynamin to regulation of the actin cytoskeleton.
  J Biol Chem, 278, 49031-49043.  
12719429 M.C.Schlumberger, A.Friebel, G.Buchwald, K.Scheffzek, A.Wittinghofer, and W.D.Hardt (2003).
Amino acids of the bacterial toxin SopE involved in G nucleotide exchange on Cdc42.
  J Biol Chem, 278, 27149-27159.  
12970366 R.P.Mohney, M.Das, T.G.Bivona, R.Hanes, A.G.Adams, M.R.Philips, and J.P.O'Bryan (2003).
Intersectin activates Ras but stimulates transcription through an independent pathway involving JNK.
  J Biol Chem, 278, 47038-47045.  
12401782 K.L.Rossman, D.K.Worthylake, J.T.Snyder, L.Cheng, I.P.Whitehead, and J.Sondek (2002).
Functional analysis of cdc42 residues required for Guanine nucleotide exchange.
  J Biol Chem, 277, 50893-50898.  
12215546 L.Cheng, K.L.Rossman, G.M.Mahon, D.K.Worthylake, M.Korus, J.Sondek, and I.P.Whitehead (2002).
RhoGEF specificity mutants implicate RhoA as a target for Dbs transforming activity.
  Mol Cell Biol, 22, 6895-6905.  
12177050 T.R.Palmby, K.Abe, and C.J.Der (2002).
Critical role of the pleckstrin homology and cysteine-rich domains in Vav signaling and transforming activity.
  J Biol Chem, 277, 39350-39359.  
12221096 W.T.Arthur, S.M.Ellerbroek, C.J.Der, K.Burridge, and K.Wennerberg (2002).
XPLN, a guanine nucleotide exchange factor for RhoA and RhoB, but not RhoC.
  J Biol Chem, 277, 42964-42972.  
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.