SMTL ID : 3kq6.1

Enhancing the Therapeutic Properties of a Protein by a Designed Zinc-Binding Site, Structural principles of a novel long-acting insulin analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-6-6-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.4, H.8 Ligands: CL.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.4, A:H.8 ZN.3: 5 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: ZN.9, ZN.15 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.5: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: CL.6, ZN.11, CL.12, ZN.17, CL.18 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.7: 3 residues within 4Å: Chain E: H.4, H.8 Ligands: CL.8 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.4, E:H.8 ZN.9: 5 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: ZN.3, ZN.15 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.11: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: ZN.5, CL.6, CL.12, ZN.17, CL.18 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.13: 3 residues within 4Å: Chain I: H.4, H.8 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.4, I:H.8 ZN.15: 5 residues within 4Å: Chain B: H.10 Chain F: H.10 Chain J: H.10 Ligands: ZN.3, ZN.9 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.17: 8 residues within 4Å: Chain D: H.10 Chain H: H.10 Chain L: H.10 Ligands: ZN.5, CL.6, ZN.11, CL.12, CL.18 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 1 interactions with chain L Metal complexes: D:H.10, H:H.10, L:H.10

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

CL.2: 3 residues within 4Å: Chain A: H.4, H.8 Ligands: ZN.1 Ligand excluded by PLIP CL.6: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.5, ZN.11, CL.12, ZN.17, CL.18 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain E: H.4, H.8 Ligands: ZN.7 Ligand excluded by PLIP CL.12: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.5, CL.6, ZN.11, ZN.17, CL.18 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain I: H.4, H.8 Ligands: ZN.13 Ligand excluded by PLIP CL.18: 11 residues within 4Å: Chain D: L.6, H.10 Chain H: L.6, H.10 Chain L: L.6, H.10 Ligands: ZN.5, CL.6, ZN.11, CL.12, ZN.17 Ligand excluded by PLIP

3 x IPH: PHENOL(Non-covalent)

IPH.4: 10 residues within 4Å: Chain C: C.6, S.9, I.10, C.11, L.16 Chain D: H.10, L.11, A.14 Chain L: H.5, L.6 8 PLIP interactions: 2 interactions with chain L, 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: L:L.6, C:L.16, D:H.10, D:L.11, D:A.14 pi-Stacking: L:H.5 Hydrogen bonds: C:C.6, C:C.11 IPH.10: 10 residues within 4Å: Chain D: H.5, L.6 Chain G: C.6, S.9, I.10, C.11, L.16 Chain H: H.10, L.11, A.14 8 PLIP interactions: 2 interactions with chain D, 3 interactions with chain H, 3 interactions with chain G Hydrophobic interactions: D:L.6, H:H.10, H:L.11, H:A.14, G:L.16 pi-Stacking: D:H.5 Hydrogen bonds: G:C.6, G:C.11 IPH.16: 10 residues within 4Å: Chain H: H.5, L.6 Chain K: C.6, S.9, I.10, C.11, L.16 Chain L: H.10, L.11, A.14 8 PLIP interactions: 3 interactions with chain L, 2 interactions with chain H, 3 interactions with chain K Hydrophobic interactions: L:H.10, L:L.11, L:A.14, H:L.6, K:L.16 pi-Stacking: H:H.5 Hydrogen bonds: K:C.6, K:C.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, N.B. et al., Supramolecular protein engineering: design of zinc-stapled insulin hexamers as a long acting depot. J.Biol.Chem. (2010)

Release Date

2010-02-23

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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