SMTL ID : 5mt9.2 (3 other biounits)

Human insulin in complex with serotonin and arginine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-6-6-mer

Ligands

6 x SRO: SEROTONIN(Non-covalent)

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

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain B: H.10 Chain H: H.10 Chain J: H.10 Ligands: CL.3, ARG.4, ARG.9 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain H, 1 interactions with chain B Metal complexes: J:H.10, H:H.10, B:H.10 ZN.6: 4 residues within 4Å: Chain D: H.10 Chain F: H.10 Chain L: H.10 Ligands: CL.13 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain L, 1 interactions with chain F Metal complexes: D:H.10, L:H.10, F:H.10

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

CL.3: 7 residues within 4Å: Chain B: H.10 Chain H: H.10 Chain J: H.10 Ligands: ZN.2, ARG.4, ARG.9, ARG.11 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain D: L.6, H.10 Chain F: H.10 Chain L: H.10 Ligands: ZN.6 Ligand excluded by PLIP

3 x ARG: ARGININE(Non-covalent)

ARG.4: 11 residues within 4Å: Chain B: H.5, L.6, C.7, H.10, E.13 Chain J: S.9, H.10 Chain L: Y.16, L.17 Ligands: ZN.2, CL.3 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain J Hydrophobic interactions: B:H.10 Hydrogen bonds: B:H.5, B:C.7, J:S.9, J:S.9 Salt bridges: B:H.10, B:E.13 ARG.9: 11 residues within 4Å: Chain B: S.9 Chain D: Y.16, L.17 Chain H: H.5, L.6, C.7, H.10, E.13, A.14 Ligands: ZN.2, CL.3 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain H, Hydrogen bonds: B:S.9, B:S.9, B:S.9, H:H.5, H:C.7, H:A.14 Salt bridges: B:H.10, H:H.10, H:E.13 Hydrophobic interactions: H:L.6, H:H.10 ARG.11: 9 residues within 4Å: Chain F: Y.16, L.17 Chain H: S.9 Chain J: H.5, L.6, C.7, H.10, E.13 Ligands: CL.3 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain H Hydrophobic interactions: J:H.10 Hydrogen bonds: J:C.7, H:S.9, H:S.9 Salt bridges: J:H.5, J:H.10, J:E.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palivec, V. et al., Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules. J. Biol. Chem. (2017)

Release Date

2017-04-05

Peptides

Insulin: ACEGIK
Insulin: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

E
I

G
K

I
M

K
O

B
F

D
H

F
J

H
L

J
N

L
P

Insulin

Insulin

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