SMTL ID : 8d1j.1

hBest1 5mM Ca2+ (Ca2+-bound) closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: Q.293, N.296, D.301, D.304 Chain C: A.10 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:N.296, A:D.301, A:D.304, C:A.10, H2O.14 CA.10: 5 residues within 4Å: Chain B: Q.293, N.296, D.301, D.304 Chain D: A.10 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:N.296, B:D.301, B:D.304, D:A.10, H2O.20 CA.20: 5 residues within 4Å: Chain B: A.10 Chain C: Q.293, N.296, D.301, D.304 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:N.296, C:D.301, C:D.304, B:A.10, H2O.8 CA.29: 5 residues within 4Å: Chain D: Q.293, N.296, D.301, D.304 Chain E: A.10 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:A.10, D:N.296, D:D.301, D:D.304, H2O.27 CA.38: 5 residues within 4Å: Chain A: A.10 Chain E: Q.293, N.296, D.301, D.304 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:A.10, E:N.296, E:D.301, E:D.304, H2O.2

40 x MC3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

MC3.2: 3 residues within 4Å: Chain A: W.24, Y.33 Ligands: MC3.3 Ligand excluded by PLIP MC3.3: 7 residues within 4Å: Chain A: L.22, C.23, W.24, R.25, Y.29, Y.33 Ligands: MC3.2 Ligand excluded by PLIP MC3.4: 5 residues within 4Å: Chain A: L.54, Q.58, M.61, F.62, V.253 Ligand excluded by PLIP MC3.5: 4 residues within 4Å: Chain A: I.38 Chain C: L.14 Ligands: MC3.19, MC3.27 Ligand excluded by PLIP MC3.6: 6 residues within 4Å: Chain A: L.40, Y.44, R.47, V.272, V.273, F.278 Ligand excluded by PLIP MC3.7: 2 residues within 4Å: Chain A: V.272, V.273 Ligand excluded by PLIP MC3.8: 7 residues within 4Å: Chain A: R.13, L.14 Chain E: Y.33, G.34, L.37, I.38 Ligands: MC3.42 Ligand excluded by PLIP MC3.9: 13 residues within 4Å: Chain A: L.14, G.15, S.18, R.19, L.21, L.22 Chain E: I.38, F.39, Y.245, S.246, L.249, L.252 Ligands: MC3.42 Ligand excluded by PLIP MC3.11: 3 residues within 4Å: Chain B: W.24, Y.33 Ligands: MC3.12 Ligand excluded by PLIP MC3.12: 7 residues within 4Å: Chain B: L.22, C.23, W.24, R.25, Y.29, Y.33 Ligands: MC3.11 Ligand excluded by PLIP MC3.13: 5 residues within 4Å: Chain B: L.54, Q.58, M.61, F.62, V.253 Ligand excluded by PLIP MC3.14: 4 residues within 4Å: Chain B: I.38 Chain D: L.14 Ligands: MC3.28, MC3.36 Ligand excluded by PLIP MC3.15: 6 residues within 4Å: Chain B: L.40, Y.44, R.47, V.272, V.273, F.278 Ligand excluded by PLIP MC3.16: 2 residues within 4Å: Chain B: V.272, V.273 Ligand excluded by PLIP MC3.17: 7 residues within 4Å: Chain B: R.13, L.14 Chain C: Y.33, G.34, L.37, I.38 Ligands: MC3.24 Ligand excluded by PLIP MC3.18: 13 residues within 4Å: Chain B: L.14, G.15, S.18, R.19, L.21, L.22 Chain C: I.38, F.39, Y.245, S.246, L.249, L.252 Ligands: MC3.24 Ligand excluded by PLIP MC3.19: 13 residues within 4Å: Chain A: I.38, F.39, Y.245, S.246, L.249, L.252 Chain C: L.14, G.15, S.18, R.19, L.21, L.22 Ligands: MC3.5 Ligand excluded by PLIP MC3.21: 3 residues within 4Å: Chain C: W.24, Y.33 Ligands: MC3.22 Ligand excluded by PLIP MC3.22: 7 residues within 4Å: Chain C: L.22, C.23, W.24, R.25, Y.29, Y.33 Ligands: MC3.21 Ligand excluded by PLIP MC3.23: 5 residues within 4Å: Chain C: L.54, Q.58, M.61, F.62, V.253 Ligand excluded by PLIP MC3.24: 4 residues within 4Å: Chain B: L.14 Chain C: I.38 Ligands: MC3.17, MC3.18 Ligand excluded by PLIP MC3.25: 6 residues within 4Å: Chain C: L.40, Y.44, R.47, V.272, V.273, F.278 Ligand excluded by PLIP MC3.26: 2 residues within 4Å: Chain C: V.272, V.273 Ligand excluded by PLIP MC3.27: 7 residues within 4Å: Chain A: Y.33, G.34, L.37, I.38 Chain C: R.13, L.14 Ligands: MC3.5 Ligand excluded by PLIP MC3.28: 13 residues within 4Å: Chain B: I.38, F.39, Y.245, S.246, L.249, L.252 Chain D: L.14, G.15, S.18, R.19, L.21, L.22 Ligands: MC3.14 Ligand excluded by PLIP MC3.30: 3 residues within 4Å: Chain D: W.24, Y.33 Ligands: MC3.31 Ligand excluded by PLIP MC3.31: 7 residues within 4Å: Chain D: L.22, C.23, W.24, R.25, Y.29, Y.33 Ligands: MC3.30 Ligand excluded by PLIP MC3.32: 5 residues within 4Å: Chain D: L.54, Q.58, M.61, F.62, V.253 Ligand excluded by PLIP MC3.33: 4 residues within 4Å: Chain D: I.38 Chain E: L.14 Ligands: MC3.37, MC3.45 Ligand excluded by PLIP MC3.34: 6 residues within 4Å: Chain D: L.40, Y.44, R.47, V.272, V.273, F.278 Ligand excluded by PLIP MC3.35: 2 residues within 4Å: Chain D: V.272, V.273 Ligand excluded by PLIP MC3.36: 7 residues within 4Å: Chain B: Y.33, G.34, L.37, I.38 Chain D: R.13, L.14 Ligands: MC3.14 Ligand excluded by PLIP MC3.37: 13 residues within 4Å: Chain D: I.38, F.39, Y.245, S.246, L.249, L.252 Chain E: L.14, G.15, S.18, R.19, L.21, L.22 Ligands: MC3.33 Ligand excluded by PLIP MC3.39: 3 residues within 4Å: Chain E: W.24, Y.33 Ligands: MC3.40 Ligand excluded by PLIP MC3.40: 7 residues within 4Å: Chain E: L.22, C.23, W.24, R.25, Y.29, Y.33 Ligands: MC3.39 Ligand excluded by PLIP MC3.41: 5 residues within 4Å: Chain E: L.54, Q.58, M.61, F.62, V.253 Ligand excluded by PLIP MC3.42: 4 residues within 4Å: Chain A: L.14 Chain E: I.38 Ligands: MC3.8, MC3.9 Ligand excluded by PLIP MC3.43: 6 residues within 4Å: Chain E: L.40, Y.44, R.47, V.272, V.273, F.278 Ligand excluded by PLIP MC3.44: 2 residues within 4Å: Chain E: V.272, V.273 Ligand excluded by PLIP MC3.45: 7 residues within 4Å: Chain D: Y.33, G.34, L.37, I.38 Chain E: R.13, L.14 Ligands: MC3.33 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Owji, A.P. et al., Structures and gating mechanisms of human bestrophin anion channels. Nat Commun (2022)

Release Date

2022-07-13

Peptides

Bestrophin-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Bestrophin-1

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