SMTL ID : 2omh.1 (1 other biounit)

Structure of human insulin cocrystallized with ARG-12 peptide in presence of urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

hetero-6-6-mer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: N.18, C.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18 Water bridges: A:C.20 NA.13: 2 residues within 4Å: Chain G: N.18, C.20 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.18 Water bridges: G:C.20

6 x RCO: RESORCINOL(Non-covalent)

RCO.2: 11 residues within 4Å: Chain A: C.6, S.9, I.10, C.11, L.16 Chain B: C.7, L.11, A.14 Chain D: H.5, L.6 Chain H: L.17 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:L.6, B:L.11 Water bridges: D:H.5 pi-Stacking: D:H.5 Hydrogen bonds: A:C.11 RCO.6: 12 residues within 4Å: Chain C: C.6, S.9, I.10, C.11, L.16 Chain D: C.7, H.10, L.11, A.14 Chain F: H.5, L.6 Chain L: L.17 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: D:H.10, D:L.11, F:L.6 Hydrogen bonds: C:C.11 RCO.9: 12 residues within 4Å: Chain B: H.5, L.6 Chain E: C.6, S.9, I.10, C.11, L.16 Chain F: C.7, H.10, L.11, A.14 Chain J: L.17 7 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B, 2 interactions with chain E Hydrophobic interactions: F:H.10, F:L.11, B:L.6 Water bridges: F:A.14, B:H.5 Hydrogen bonds: E:C.11, E:C.11 RCO.14: 11 residues within 4Å: Chain B: L.17 Chain G: C.6, S.9, I.10, C.11, L.16 Chain H: C.7, L.11, A.14 Chain J: H.5, L.6 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: J:L.6, H:L.11 Water bridges: J:H.5 pi-Stacking: J:H.5 Hydrogen bonds: G:C.11 RCO.18: 12 residues within 4Å: Chain F: L.17 Chain I: C.6, S.9, I.10, C.11, L.16 Chain J: C.7, H.10, L.11, A.14 Chain L: H.5, L.6 4 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: J:H.10, J:L.11, L:L.6 Hydrogen bonds: I:C.11 RCO.21: 12 residues within 4Å: Chain D: L.17 Chain H: H.5, L.6 Chain K: C.6, S.9, I.10, C.11, L.16 Chain L: C.7, H.10, L.11, A.14 7 PLIP interactions: 3 interactions with chain L, 2 interactions with chain H, 2 interactions with chain K Hydrophobic interactions: L:H.10, L:L.11, H:L.6 Water bridges: L:A.14, H:H.5 Hydrogen bonds: K:C.11, K:C.11

8 x URE: UREA(Non-functional Binders)

URE.3: 5 residues within 4Å: Chain A: Q.5, S.9, I.10, C.11, Q.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.5, A:I.10, A:Q.15 Water bridges: A:Q.5 URE.7: 5 residues within 4Å: Chain C: Q.5, S.9, I.10, C.11, Q.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.5, C:I.10, C:Q.15 Water bridges: C:S.12 URE.10: 5 residues within 4Å: Chain E: Q.5, S.9, I.10, C.11, Q.15 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.5, E:Q.5, E:Q.15 URE.11: 4 residues within 4Å: Chain F: Y.16, L.17, G.20 Chain L: H.5 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain L Hydrogen bonds: F:Y.16, F:Y.16, F:G.20 Water bridges: L:H.5, L:H.5 URE.15: 5 residues within 4Å: Chain G: Q.5, S.9, I.10, C.11, Q.15 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:Q.5, G:I.10, G:Q.15 Water bridges: G:Q.5 URE.19: 5 residues within 4Å: Chain I: Q.5, S.9, I.10, C.11, Q.15 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:Q.5, I:I.10, I:Q.15 Water bridges: I:S.12 URE.22: 5 residues within 4Å: Chain K: Q.5, S.9, I.10, C.11, Q.15 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:Q.5, K:Q.5, K:Q.15 URE.23: 4 residues within 4Å: Chain F: H.5 Chain L: Y.16, L.17, G.20 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:Y.16, L:Y.16, L:G.20

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain B: H.10 Chain D: H.10 Chain F: H.10 Ligands: CL.5 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain D Metal complexes: B:H.10, F:H.10, D:H.10 ZN.16: 4 residues within 4Å: Chain H: H.10 Chain J: H.10 Chain L: H.10 Ligands: CL.17 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain L, 1 interactions with chain H Metal complexes: J:H.10, L:H.10, H:H.10

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 7 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain H: L.6, H.10 Chain J: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.16 Ligand excluded by PLIP

4 x ARF: FORMAMIDE(Covalent)

ARF.8: 4 residues within 4Å: Chain D: F.1, V.2, N.3, Q.4 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.4 Water bridges: D:N.3, D:N.3 ARF.12: 5 residues within 4Å: Chain C: T.8, S.9, I.10 Chain F: F.1, V.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain F Hydrogen bonds: C:I.10 Water bridges: F:F.1, F:F.1 ARF.20: 4 residues within 4Å: Chain J: F.1, V.2, N.3, Q.4 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:Q.4 Water bridges: J:N.3, J:N.3 ARF.24: 5 residues within 4Å: Chain I: T.8, S.9, I.10 Chain L: F.1, V.2 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain I Water bridges: L:F.1, L:F.1 Hydrogen bonds: I:I.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Norrman, M. et al., Structural characterization of insulin NPH formulations. EUR.J.PHARM.SCI. (2007)

Release Date

2007-03-27

Peptides

Insulin A chain: ACEGIK
Insulin B chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
A

I
C

K
E

B
B

D
D

F
F

H
B

J
D

L
F

Insulin A chain

Insulin B chain

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