SMTL ID : 8pi5.1

Crystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in hexamer (T3R3) conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 9 residues within 4Å: Chain A: H.5, H.10 Chain C: H.10 Chain E: H.10 Ligands: ZN.3, ZN.7, ZN.9, ZN.13, ZN.15 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.10, E:H.10, C:H.10, H2O.2, H2O.5 ZN.2: 7 residues within 4Å: Chain B: E.13 Chain C: E.13 Chain D: E.13 Chain E: E.13 Chain F: E.13 Ligands: ZN.8, ZN.14 No protein-ligand interaction detected (PLIP) ZN.3: 11 residues within 4Å: Chain A: H.5, C.7 Chain C: H.5, C.7 Chain E: H.5, C.7 Ligands: ZN.1, ZN.7, ZN.9, ZN.13, ZN.15 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: E:H.5, A:H.5, C:H.5, H2O.2, H2O.5 ZN.4: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: CL.5, ZN.10, CL.11, ZN.16, CL.17 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B Metal complexes: D:H.10, F:H.10, B:H.10 ZN.7: 9 residues within 4Å: Chain A: H.10 Chain C: H.5, H.10 Chain E: H.10 Ligands: ZN.1, ZN.3, ZN.9, ZN.13, ZN.15 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.10, E:H.10, C:H.10, H2O.2, H2O.5 ZN.8: 7 residues within 4Å: Chain A: E.13 Chain B: E.13 Chain D: E.13 Chain E: E.13 Chain F: E.13 Ligands: ZN.2, ZN.14 No protein-ligand interaction detected (PLIP) ZN.9: 11 residues within 4Å: Chain A: H.5, C.7 Chain C: H.5, C.7 Chain E: H.5, C.7 Ligands: ZN.1, ZN.3, ZN.7, ZN.13, ZN.15 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: E:H.5, A:H.5, C:H.5, H2O.2, H2O.5 ZN.10: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4, CL.5, CL.11, ZN.16, CL.17 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B Metal complexes: D:H.10, F:H.10, B:H.10 ZN.13: 9 residues within 4Å: Chain A: H.10 Chain C: H.10 Chain E: H.5, H.10 Ligands: ZN.1, ZN.3, ZN.7, ZN.9, ZN.15 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.10, E:H.10, C:H.10, H2O.2, H2O.5 ZN.14: 7 residues within 4Å: Chain A: E.13 Chain B: E.13 Chain C: E.13 Chain D: E.13 Chain F: E.13 Ligands: ZN.2, ZN.8 No protein-ligand interaction detected (PLIP) ZN.15: 11 residues within 4Å: Chain A: H.5, C.7 Chain C: H.5, C.7 Chain E: H.5, C.7 Ligands: ZN.1, ZN.3, ZN.7, ZN.9, ZN.13 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: E:H.5, A:H.5, C:H.5, H2O.2, H2O.5 ZN.16: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4, CL.5, ZN.10, CL.11, CL.17 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain F Metal complexes: D:H.10, B:H.10, F:H.10

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

CL.5: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4, ZN.10, CL.11, ZN.16, CL.17 Ligand excluded by PLIP CL.11: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4, CL.5, ZN.10, ZN.16, CL.17 Ligand excluded by PLIP CL.17: 11 residues within 4Å: Chain B: L.6, H.10 Chain D: L.6, H.10 Chain F: L.6, H.10 Ligands: ZN.4, CL.5, ZN.10, CL.11, ZN.16 Ligand excluded by PLIP

3 x RCO: RESORCINOL(Non-covalent)

RCO.6: 15 residues within 4Å: Chain B: C.7, H.10, L.11, A.14, C.38, C.39, S.41, I.42, C.43, L.45, L.48 Chain E: L.17 Chain F: V.2, H.5, L.6 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:L.11, F:L.6 Hydrogen bonds: B:C.38, B:C.43, F:H.5 RCO.12: 15 residues within 4Å: Chain A: L.17 Chain B: V.2, H.5, L.6 Chain D: C.7, H.10, L.11, A.14, C.38, C.39, S.41, I.42, C.43, L.45, L.48 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.11, B:L.6 Hydrogen bonds: D:C.38, D:C.43, B:H.5 RCO.18: 15 residues within 4Å: Chain C: L.17 Chain D: V.2, H.5, L.6 Chain F: C.7, H.10, L.11, A.14, C.38, C.39, S.41, I.42, C.43, L.45, L.48 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:L.6, F:L.11 Hydrogen bonds: D:H.5, F:C.38, F:C.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kjeldsen, T. et al., Molecular engineering of insulin for recombinant expression in yeast. Trends Biotechnol (2024)

Release Date

2023-11-08

Peptides

Insulin B chain,Insulin A chain: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
B

D
D

E
B

F
D

Insulin B chain,Insulin A chain

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