SMTL ID : 6ivm.1

Crystal structure of a membrane protein P143A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-pentamer

Ligands

17 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: E.194 Chain E: H.197 Ligands: CL.5 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:E.194, E:H.197, H2O.3 ZN.2: 3 residues within 4Å: Chain A: H.197 Chain B: E.194 Ligands: CL.13 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.197, B:E.194, B:E.194, H2O.1 ZN.3: 4 residues within 4Å: Chain A: H.111, H.114 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.111, A:H.114 ZN.4: 4 residues within 4Å: Chain A: D.264, G.267, A.269, D.272 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.264, A:D.272, H2O.1 ZN.10: 1 residues within 4Å: Chain B: H.238 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.238, H2O.2 ZN.11: 4 residues within 4Å: Chain B: H.197 Chain D: K.191, E.194 Ligands: CL.28 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.194, D:E.194, B:H.197, H2O.3 ZN.12: 4 residues within 4Å: Chain B: H.111, H.114, H.293 Ligands: ACY.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.111, B:H.114, B:H.293, ACY.14 ZN.15: 4 residues within 4Å: Chain C: K.191, E.194 Chain D: H.197 Ligands: CL.18 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.197, C:E.194, C:E.194, H2O.2 ZN.16: 5 residues within 4Å: Chain C: D.193, H.197 Chain E: K.191, E.194 Ligands: CL.34 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:D.193, C:H.197, E:E.194, E:E.194, H2O.2 ZN.17: 3 residues within 4Å: Chain C: H.111, H.114 Ligands: CL.19 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.111, C:H.114, H2O.2 ZN.20: 1 residues within 4Å: Chain C: H.54 No protein-ligand interaction detected (PLIP) ZN.23: 4 residues within 4Å: Chain D: H.111, H.114 Ligands: CL.26, CL.27 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.111, D:H.114 ZN.24: 1 residues within 4Å: Chain D: D.136 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.136 ZN.25: 1 residues within 4Å: Chain D: D.112 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.112 ZN.30: 4 residues within 4Å: Chain E: H.111, H.114 Ligands: CL.32, CL.33 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.111, E:H.114 ZN.31: 3 residues within 4Å: Chain E: D.288, H.293 Ligands: ACY.22 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.288, E:H.293 ZN.35: 2 residues within 4Å: Chain E: G.235, H.238 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.238

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

CL.5: 6 residues within 4Å: Chain A: T.98, K.191, E.194 Chain E: D.193, H.197 Ligands: ZN.1 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: H.111, R.115, Q.292 Ligands: ZN.3, CL.7 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: R.104, H.111, H.114 Ligands: ZN.3, CL.6 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain A: D.193, H.197 Chain B: T.98, K.191, E.194 Ligands: ZN.2 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain C: T.98, K.191, E.194 Chain D: H.197 Ligands: ZN.15 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain C: R.104, H.111, H.114, M.289, T.290 Ligands: ZN.17 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain D: R.104, H.111, H.114, T.290 Ligands: ZN.23, CL.27 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain D: H.111, H.114, R.115 Ligands: ZN.23, CL.26 Ligand excluded by PLIP CL.28: 6 residues within 4Å: Chain B: D.193, H.197 Chain D: T.98, K.191, E.194 Ligands: ZN.11 Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain E: H.111, H.114, R.115, T.290 Ligands: ZN.30, CL.33 Ligand excluded by PLIP CL.33: 6 residues within 4Å: Chain E: R.104, H.111, H.114, T.290 Ligands: ZN.30, CL.32 Ligand excluded by PLIP CL.34: 8 residues within 4Å: Chain C: D.193, H.197 Chain E: I.94, A.95, T.98, K.191, E.194 Ligands: ZN.16 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: Y.79, W.255, L.258 Chain E: R.74, A.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.75

1 x LEU: LEUCINE(Non-covalent)

LEU.9: 3 residues within 4Å: Chain A: N.169, Q.173 Chain B: P.294 1 PLIP interactions: 1 interactions with chain A, Hydrophobic interactions: A:Q.173

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.14: 6 residues within 4Å: Chain B: R.104, H.111, H.114, R.115, G.291 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.104, B:H.114, B:H.293 ACY.22: 4 residues within 4Å: Chain C: S.157 Chain E: R.284, H.293 Ligands: ZN.31 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:R.284 Salt bridges: E:H.293

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.21: 9 residues within 4Å: Chain C: F.73, R.74, S.76, A.77, S.80 Chain E: N.75, S.76, Y.79, L.258 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.29: 4 residues within 4Å: Chain C: Q.102 Chain D: D.189, N.190, D.193 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.102, D:D.189, D:D.189 Water bridges: C:K.191

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

Ibestrophin: 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.
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Ibestrophin