SMTL ID : 6ivp.1

Crystal structure of a membrane protein P262A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

homo-pentamer

Ligands

14 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: K.191, E.194 Chain E: H.197 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Metal complexes: A:E.194, E:H.197 ZN.2: 3 residues within 4Å: Chain A: H.197 Chain B: E.194 Ligands: CL.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.194, B:E.194, A:H.197 ZN.3: 3 residues within 4Å: Chain A: H.111, H.114 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.111, A:H.114 ZN.6: 3 residues within 4Å: Chain B: Y.45, H.238 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.238 ZN.7: 5 residues within 4Å: Chain B: H.111, H.114, G.291, H.293 Ligands: CL.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.111, B:H.114, B:H.293 ZN.10: 4 residues within 4Å: Chain B: H.197 Chain D: K.191, E.194 Ligands: CL.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.194, D:E.194, B:H.197 ZN.11: 4 residues within 4Å: Chain C: K.191, E.194 Chain D: H.197 Ligands: CL.13 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.194, C:E.194, D:H.197, H2O.1 ZN.12: 3 residues within 4Å: Chain C: H.111, H.114 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.111, C:H.114 ZN.15: 2 residues within 4Å: Chain C: E.49, H.54 No protein-ligand interaction detected (PLIP) ZN.16: 3 residues within 4Å: Chain C: H.197 Chain E: K.191, E.194 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Metal complexes: C:H.197, E:E.194, E:E.194 ZN.17: 4 residues within 4Å: Chain D: H.111, H.114 Ligands: CL.21, CL.22 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.111, D:H.114 ZN.18: 2 residues within 4Å: Chain D: D.136, T.138 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.136 ZN.19: 1 residues within 4Å: Chain D: D.112 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.112 ZN.23: 3 residues within 4Å: Chain E: H.111, H.114 Ligands: CL.24 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.111, E:H.114

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

CL.4: 4 residues within 4Å: Chain A: H.111, H.114, R.115 Ligands: ZN.3 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: H.197 Chain B: T.98, K.191, E.194 Ligands: ZN.2 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: I.42 Ligands: ZN.6 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: H.111, H.114, R.115, G.291 Ligands: ZN.7 Ligand excluded by PLIP CL.13: 7 residues within 4Å: Chain C: I.94, A.95, T.98, K.191, E.194 Chain D: H.197 Ligands: ZN.11 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: R.104, H.111, H.114, T.290 Ligands: ZN.12 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: H.197 Chain D: I.94, T.98, K.191, E.194 Ligands: ZN.10 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain D: R.104, H.111, H.114, T.290 Ligands: ZN.17 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain D: H.111, H.114, R.115, T.290 Ligands: ZN.17 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain E: H.111, H.114, T.290 Ligands: ZN.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, C. et al., Dual Ca2+-dependent gates in human Bestrophin1 underlie disease-causing mechanisms of gain-of-function mutations. Commun Biol (2019)

Release Date

2019-11-06

Peptides

bestrophin: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
Show / Hide

bestrophin