SMTL ID : 8ipz.1 (1 other biounit)

Crystal structure of insulin detemir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-6-6-mer

Ligands

6 x IPH: PHENOL(Non-covalent)

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

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 8 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: CL.3, ZN.10, CL.11, ZN.18, CL.19 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain F, 1 interactions with chain B Metal complexes: J:H.10, F:H.10, B:H.10 ZN.6: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: CL.7, ZN.14, CL.15, ZN.22, CL.23 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H, 1 interactions with chain D Metal complexes: L:H.10, H:H.10, D:H.10 ZN.10: 8 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: ZN.2, CL.3, CL.11, ZN.18, CL.19 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain F, 1 interactions with chain B Metal complexes: J:H.10, F:H.10, B:H.10 ZN.14: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: ZN.6, CL.7, CL.15, ZN.22, CL.23 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain H, 1 interactions with chain D Metal complexes: L:H.10, H:H.10, D:H.10 ZN.18: 8 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: ZN.2, CL.3, ZN.10, CL.11, CL.19 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 1 interactions with chain F Metal complexes: B:H.10, J:H.10, F:H.10 ZN.22: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: ZN.6, CL.7, ZN.14, CL.15, CL.23 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain L, 1 interactions with chain D Metal complexes: H:H.10, L:H.10, D:H.10

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

CL.3: 11 residues within 4Å: Chain B: L.6, H.10 Chain F: L.6, H.10 Chain J: L.6, H.10 Ligands: ZN.2, ZN.10, CL.11, ZN.18, CL.19 Ligand excluded by PLIP CL.7: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.6, ZN.14, CL.15, ZN.22, CL.23 Ligand excluded by PLIP CL.11: 11 residues within 4Å: Chain B: L.6, H.10 Chain F: L.6, H.10 Chain J: L.6, H.10 Ligands: ZN.2, CL.3, ZN.10, ZN.18, CL.19 Ligand excluded by PLIP CL.15: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.6, CL.7, ZN.14, ZN.22, CL.23 Ligand excluded by PLIP CL.19: 11 residues within 4Å: Chain B: L.6, H.10 Chain F: L.6, H.10 Chain J: L.6, H.10 Ligands: ZN.2, CL.3, ZN.10, CL.11, ZN.18 Ligand excluded by PLIP CL.23: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.6, CL.7, ZN.14, CL.15, ZN.22 Ligand excluded by PLIP

6 x MYR: MYRISTIC ACID(Non-covalent)(Covalent)

MYR.4: 9 residues within 4Å: Chain A: V.3, E.4, C.7 Chain B: F.1, N.3, Q.4, C.7, K.29 Chain F: N.3 6 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: B:F.1, B:N.3, B:Q.4, B:Q.4, F:N.3, A:E.4 MYR.8: 3 residues within 4Å: Chain D: F.1, Q.4, K.29 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.1, D:F.1, D:K.29 MYR.12: 9 residues within 4Å: Chain E: V.3, E.4, C.7 Chain F: F.1, N.3, Q.4, C.7, K.29 Chain J: N.3 6 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: F:F.1, F:N.3, F:Q.4, F:Q.4, E:E.4, J:N.3 MYR.16: 3 residues within 4Å: Chain H: F.1, Q.4, K.29 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.1, H:F.1, H:K.29 MYR.20: 9 residues within 4Å: Chain B: N.3 Chain I: V.3, E.4, C.7 Chain J: F.1, N.3, Q.4, C.7, K.29 6 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I, 1 interactions with chain B Hydrophobic interactions: J:F.1, J:N.3, J:Q.4, J:Q.4, I:E.4, B:N.3 MYR.24: 3 residues within 4Å: Chain L: F.1, Q.4, K.29 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.1, L:F.1, L:K.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

DeMirci, H. et al., Crystal structure of insulin detemir. To Be Published

Release Date

2023-12-13

Peptides

Insulin A chain: ACEGIK
Insulin B chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

I
A

K
C

B
B

D
D

F
B

H
D

J
B

L
D

Insulin A chain

Insulin B chain

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