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Hormone PDB id
1ben
Jmol
Contents
Protein chains
21 a.a.
30 a.a. *
28 a.a. *
Ligands
HBD ×2
Metals
_ZN ×2
_CL
Waters ×168
* Residue conservation analysis
PDB id:
1ben
Name: Hormone
Title: Insulin complexed with 4-hydroxybenzamide
Structure: Human insulin. Chain: a, c. Synonym: insulin. Engineered: yes. Human insulin. Chain: b, d. Synonym: insulin. Engineered: yes
Source: Synthetic: yes. Other_details: gift of lilly research laboratories. Other_details: gift of lilly research laboratories
Biol. unit: Dodecamer (from PDB file)
Resolution:
1.40Å     R-factor:   0.154    
Authors: G.D.Smith,E.Ciszak,W.Pangborn
Key ref:
G.D.Smith et al. (1996). A novel complex of a phenolic derivative with insulin: structural features related to the T-->R transition. Protein Sci, 5, 1502-1511. PubMed id: 8844841 Ref: Full text
Date:
15-Feb-96     Release date:   11-Jul-96    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc: 		110 a.a.
21 a.a.
Protein chain
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc: 		110 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P01308  (INS_HUMAN) -  Insulin
Seq:
Struc: 		110 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biochemical function     hormone activity     1 term  

 

 
Full text Protein Sci 5:1502-1511 (1996)
PubMed id: 8844841  
 
 
A novel complex of a phenolic derivative with insulin: structural features related to the T-->R transition.
G.D.Smith, E.Ciszak, W.Pangborn.
 
  ABSTRACT  
 
The structure of a symmetric T3R3f insulin hexamer, complexed with 4-hydroxybenzamide, has been determined using X-ray crystallographic techniques. Data were measured from six crystals grown in microgravity to a resolution of 1.4 A and the structure has been refined including the contributions from hydrogen atoms. The crystals are isomorphous with T3R3f complexes of phenolic derivatives as well as with uncomplexed forms. Unlike the structures of complexes with phenol, m-cresol, resorcinol, 4'-hydroxyacetanilide, and methylparaben, which bind one phenolic derivative molecule per R- or Rf-state monomer, two molecules of 4-hydroxybenzamide are bound by each Rf-state monomer. The presence of the second guest molecule results in an extensive hydrogen bonding network, mediated by water molecules, between the T- and Rf-state trimers and adds stability to the formation of the hexamer. The only access to these second sites is through three symmetry-related, narrow channels that originate on the surface of the T-state trimer. Although the conformation of the backbone atoms of the monomers is nearly identical to that of other T3R3f hexamers, significant changes are observed in the conformations of side chains in the vicinity of the second binding site. The side chain of the T-state A11 Cys residue, which forms a disulfide bond to A6 Cys in the same monomer, is observed in two discrete conformations; two discrete conformations are also present for the entire A8 Thr residue in the Rf-state monomer. A procedure is also described for an alternate method of interframe scaling and merging intensity data from an image plate detector.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereopairshowing1.50electrondensityaroundthepair of 4-hydroxybenzamide molecules in thephenolicbinding sites. The-hydroxybenzamidemoleculeintheupperportion of theillustrationresidesinbindingsite I, andthesecondguestmol- ecule resides in inding site 11. Water molecules and residues articipatinginhydrogenbonds are alsoshown. A21 lCys and BZlOHis refer toA6.2Cys,A11.2Cys,and His,respectively,and B310His and B313Glu refer to B13.1 Glu and B1O.l Hisofaneighboringdimer. 		Figure 4.
Fig. 4. Thebottomportion of bindingsite I1 as viewed alongthec-axisfromtheT-statetrimertowardtheR'-statetrimer. TheConnollysurface(Connoll, 1983) was constructedfromonlytheproteinatoms of thehexamer.The4-hydroxybenzamide molecule and B13 GluresiduesarelabeledasBNZandBnl3GLU,respectively,where n rangesbetween 1 and 6andrepresents B13.nGlu.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1996, 5, 1502-1511) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18676643 H.Vashisth, and C.F.Abrams (2008).
Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex.
  Biophys J, 95, 4193-4204.  
16239724 G.D.Smith, W.A.Pangborn, and R.H.Blessing (2005).
The structure of T6 bovine insulin.
  Acta Crystallogr D Biol Crystallogr, 61, 1476-1482.
PDB code: 2a3g
15930636 R.A.Judge, E.H.Snell, M.J.van der Woerd, and E.H.Snell (2005).
Extracting trends from two decades of microgravity macromolecular crystallization history.
  Acta Crystallogr D Biol Crystallogr, 61, 763-771.  
11914489 J.D.Ng, C.Sauter, B.Lorber, N.Kirkland, J.Arnez, and R.Giegé (2002).
Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination.
  Acta Crystallogr D Biol Crystallogr, 58, 645-652.
PDB code: 1l0w
11468392 G.D.Smith, W.A.Pangborn, and R.H.Blessing (2001).
Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced?
  Acta Crystallogr D Biol Crystallogr, 57, 1091-1100.
PDB codes: 1g7a 1g7b
11015187 F.P.Ottensmeyer, D.R.Beniac, R.Z.Luo, and C.C.Yip (2000).
Mechanism of transmembrane signaling: insulin binding and the insulin receptor.
  Biochemistry, 39, 12103-12112.  
11092919 G.D.Smith, E.Ciszak, L.A.Magrum, W.A.Pangborn, and R.H.Blessing (2000).
R6 hexameric insulin complexed with m-cresol or resorcinol.
  Acta Crystallogr D Biol Crystallogr, 56, 1541-1548.
PDB codes: 1ev3 1ev6 1evr
10397800 H.Berchtold, and R.Hilgenfeld (1999).
Binding of phenol to R6 insulin hexamers.
  Biopolymers, 51, 165-172.  
10089304 J.Dong, T.J.Boggon, N.E.Chayen, J.Raftery, R.C.Bi, and J.R.Helliwell (1999).
Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 745-752.
PDB codes: 1bvx 1bwh 1bwi 1bwj
10479347 J.P.Richards, M.P.Stickelmeyer, B.H.Frank, S.Pye, M.Barbeau, J.Radziuk, G.D.Smith, and M.R.DeFelippis (1999).
Preparation of a microcrystalline suspension formulation of Lys(B28)Pro(B29)-human insulin with ultralente properties.
  J Pharm Sci, 88, 861-867.  
18726499 S.Yao, X.Zhang, Y.Xu, X.Zhang, and S.Zhu (1999).
Insulin and insulin mutants stimulate glucose uptake in rat adipocytes.
  Sci China C Life Sci, 42, 63-67.  
9708987 J.L.Whittingham, D.J.Edwards, A.A.Antson, J.M.Clarkson, and G.G.Dodson (1998).
Interactions of phenol and m-cresol in the insulin hexamer, and their effect on the association properties of B28 pro --> Asp insulin analogues.
  Biochemistry, 37, 11516-11523.
PDB codes: 1zeg 1zeh 1zei
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.