SMTL ID : 5bqq.1

Human insulin with intra-chain chemical crosslink between modified B27 and B30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-6-6-mer

Ligands

10 x IPH: PHENOL(Non-covalent)

IPH.1: 8 residues within 4Å: Chain A: C.6, S.9, I.10, C.11 Chain B: H.10, L.11, A.14 Chain F: H.5 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: A:I.10, B:L.11, B:A.14 Hydrogen bonds: A:C.6, A:C.11 pi-Cation interactions: F:H.5 IPH.4: 8 residues within 4Å: Chain C: C.6, S.9, I.10, C.11 Chain D: H.10, L.11, A.14 Chain L: H.5 6 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D, 1 interactions with chain L Hydrophobic interactions: C:I.10, D:L.11, D:A.14 Hydrogen bonds: C:C.6, C:C.11 pi-Cation interactions: L:H.5 IPH.7: 9 residues within 4Å: Chain E: C.6, S.9, I.10, C.11 Chain F: C.7, H.10, L.11, A.14 Ligands: IPH.12 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:I.10, F:L.11, F:L.11, F:A.14 Hydrogen bonds: E:C.6, E:C.11 IPH.8: 9 residues within 4Å: Chain B: L.17 Chain D: H.5 Chain G: C.6, S.9, I.10, C.11 Chain H: H.10, L.11, A.14 6 PLIP interactions: 2 interactions with chain H, 1 interactions with chain B, 2 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: H:L.11, H:A.14, B:L.17 Hydrogen bonds: G:C.6, G:C.11 pi-Cation interactions: D:H.5 IPH.9: 9 residues within 4Å: Chain F: E.13, Y.16, L.17 Chain H: H.5, L.6, S.9 Chain L: H.10 Ligands: IPH.10, IPH.14 7 PLIP interactions: 2 interactions with chain L, 3 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: L:H.10, H:H.5, H:L.6, F:L.17 Hydrogen bonds: L:H.10, H:S.9 pi-Stacking: F:Y.16 IPH.10: 7 residues within 4Å: Chain F: Y.16, L.17, G.20, E.21 Chain H: H.5, P.28 Ligands: IPH.9 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain F Hydrophobic interactions: H:P.28, F:Y.16, F:Y.16, F:E.21 pi-Stacking: H:H.5 IPH.11: 9 residues within 4Å: Chain B: H.5 Chain D: L.17 Chain I: C.6, S.9, I.10, C.11 Chain J: H.10, L.11, A.14 6 PLIP interactions: 2 interactions with chain I, 2 interactions with chain J, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: I:C.6, I:C.11 Hydrophobic interactions: J:L.11, J:A.14, D:L.17 pi-Cation interactions: B:H.5 IPH.12: 9 residues within 4Å: Chain F: H.10 Chain J: H.5, L.6, S.9 Chain L: E.13, Y.16, L.17 Ligands: IPH.7, IPH.13 7 PLIP interactions: 2 interactions with chain L, 2 interactions with chain F, 3 interactions with chain J Hydrophobic interactions: L:L.17, F:H.10, J:H.5, J:L.6 pi-Stacking: L:Y.16 Hydrogen bonds: F:H.10, J:S.9 IPH.13: 7 residues within 4Å: Chain J: H.5, P.28 Chain L: Y.16, L.17, G.20, E.21 Ligands: IPH.12 5 PLIP interactions: 3 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:Y.16, L:Y.16, L:E.21, J:P.28 pi-Stacking: J:H.5 IPH.14: 9 residues within 4Å: Chain K: C.6, S.9, I.10, C.11 Chain L: C.7, H.10, L.11, A.14 Ligands: IPH.9 6 PLIP interactions: 3 interactions with chain L, 3 interactions with chain K Hydrophobic interactions: L:L.11, L:L.11, L:A.14, K:I.10 Hydrogen bonds: K:C.6, K:C.11

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: CL.3 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain J Metal complexes: B:H.10, F:H.10, J:H.10 ZN.5: 4 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: CL.6 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Metal complexes: L:H.10, D:H.10, H:H.10

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

CL.3: 7 residues within 4Å: Chain B: L.6, H.10 Chain F: L.6, H.10 Chain J: L.6, H.10 Ligands: ZN.2 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vikova, J. et al., Rational steering of insulin binding specificity by intra-chain chemical crosslinking. Sci Rep (2016)

Release Date

2016-02-03

Peptides

Insulin: ACEGIK
Insulin: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

B
B

D
D

F
F

H
H

J
J

L
L

Insulin

Insulin

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