SMTL ID : 8d1g.1

hBest2 Ca2+-bound open 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: 1 interactions with chain C, 4 interactions with chain A Metal complexes: C:A.10, A:Q.293, A:N.296, A:D.301, A:D.304 CA.14: 5 residues within 4Å: Chain A: A.10 Chain B: Q.293, N.296, D.301, D.304 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Metal complexes: B:Q.293, B:N.296, B:D.301, B:D.304, A:A.10 CA.27: 5 residues within 4Å: Chain C: Q.293, N.296, D.301, D.304 Chain E: A.10 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Metal complexes: C:Q.293, C:N.296, C:D.301, C:D.304, E:A.10 CA.38: 5 residues within 4Å: Chain B: A.10 Chain D: Q.293, N.296, D.301, D.304 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Metal complexes: B:A.10, D:Q.293, D:N.296, D:D.301, D:D.304 CA.51: 5 residues within 4Å: Chain D: A.10 Chain E: Q.293, N.296, D.301, D.304 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Metal complexes: E:Q.293, E:N.296, E:D.301, E:D.304, D:A.10

5 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.2: 12 residues within 4Å: Chain A: L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.5, MC3.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.46, A:L.46, A:L.54, A:Y.61, A:Y.61, A:F.62, A:L.65, A:L.249, A:L.252, A:I.253 Hydrogen bonds: A:G.57, A:G.57, A:Y.61 Water bridges: A:K.64 DU0.15: 12 residues within 4Å: Chain B: L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.18, MC3.19 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.46, B:L.46, B:L.54, B:Y.61, B:Y.61, B:F.62, B:L.65, B:L.249, B:L.252, B:I.253 Hydrogen bonds: B:G.57, B:G.57, B:Y.61 Water bridges: B:K.64 DU0.28: 12 residues within 4Å: Chain C: L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.31, MC3.32 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.46, C:L.46, C:L.54, C:Y.61, C:Y.61, C:F.62, C:L.65, C:L.249, C:L.252, C:I.253 Hydrogen bonds: C:G.57, C:G.57, C:Y.61 Water bridges: C:K.64 DU0.39: 12 residues within 4Å: Chain D: L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.42, MC3.43 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.46, D:L.46, D:L.54, D:Y.61, D:Y.61, D:F.62, D:L.65, D:L.249, D:L.252, D:I.253 Hydrogen bonds: D:G.57, D:G.57, D:Y.61 Water bridges: D:K.64 DU0.52: 12 residues within 4Å: Chain E: L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.55, MC3.56 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:L.46, E:L.46, E:L.54, E:Y.61, E:Y.61, E:F.62, E:L.65, E:L.249, E:L.252, E:I.253 Hydrogen bonds: E:G.57, E:G.57, E:Y.61 Water bridges: E:K.64

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

MC3.3: 8 residues within 4Å: Chain A: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.4 Ligand excluded by PLIP MC3.4: 8 residues within 4Å: Chain A: L.21, L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.3, MC3.12 Ligand excluded by PLIP MC3.5: 4 residues within 4Å: Chain A: Y.61, L.65 Ligands: DU0.2, MC3.36 Ligand excluded by PLIP MC3.6: 3 residues within 4Å: Chain A: A.45, Q.58 Ligands: DU0.2 Ligand excluded by PLIP MC3.7: 2 residues within 4Å: Chain A: A.45 Ligands: MC3.8 Ligand excluded by PLIP MC3.8: 6 residues within 4Å: Chain A: G.41, M.44, A.45, F.52 Ligands: MC3.7, MC3.11 Ligand excluded by PLIP MC3.9: 4 residues within 4Å: Chain A: R.34, L.37, C.38 Chain C: F.14 Ligand excluded by PLIP MC3.10: 4 residues within 4Å: Chain A: D.270, L.271, C.272 Ligands: MC3.18 Ligand excluded by PLIP MC3.11: 1 residues within 4Å: Ligands: MC3.8 Ligand excluded by PLIP MC3.12: 16 residues within 4Å: Chain A: F.14, G.15, S.18, Q.19, L.21, L.22 Chain B: E.35, C.38, F.39, F.42, Y.245, S.246, F.248, L.249, L.252 Ligands: MC3.4 Ligand excluded by PLIP MC3.16: 8 residues within 4Å: Chain B: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.17 Ligand excluded by PLIP MC3.17: 8 residues within 4Å: Chain B: L.21, L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.16, MC3.25 Ligand excluded by PLIP MC3.18: 4 residues within 4Å: Chain B: Y.61, L.65 Ligands: MC3.10, DU0.15 Ligand excluded by PLIP MC3.19: 3 residues within 4Å: Chain B: A.45, Q.58 Ligands: DU0.15 Ligand excluded by PLIP MC3.20: 2 residues within 4Å: Chain B: A.45 Ligands: MC3.21 Ligand excluded by PLIP MC3.21: 6 residues within 4Å: Chain B: G.41, M.44, A.45, F.52 Ligands: MC3.20, MC3.24 Ligand excluded by PLIP MC3.22: 4 residues within 4Å: Chain A: F.14 Chain B: R.34, L.37, C.38 Ligand excluded by PLIP MC3.23: 4 residues within 4Å: Chain B: D.270, L.271, C.272 Ligands: MC3.42 Ligand excluded by PLIP MC3.24: 1 residues within 4Å: Ligands: MC3.21 Ligand excluded by PLIP MC3.25: 16 residues within 4Å: Chain B: F.14, G.15, S.18, Q.19, L.21, L.22 Chain D: E.35, C.38, F.39, F.42, Y.245, S.246, F.248, L.249, L.252 Ligands: MC3.17 Ligand excluded by PLIP MC3.26: 16 residues within 4Å: Chain A: E.35, C.38, F.39, F.42, Y.245, S.246, F.248, L.249, L.252 Chain C: F.14, G.15, S.18, Q.19, L.21, L.22 Ligands: MC3.30 Ligand excluded by PLIP MC3.29: 8 residues within 4Å: Chain C: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.30 Ligand excluded by PLIP MC3.30: 8 residues within 4Å: Chain C: L.21, L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.26, MC3.29 Ligand excluded by PLIP MC3.31: 4 residues within 4Å: Chain C: Y.61, L.65 Ligands: DU0.28, MC3.60 Ligand excluded by PLIP MC3.32: 3 residues within 4Å: Chain C: A.45, Q.58 Ligands: DU0.28 Ligand excluded by PLIP MC3.33: 2 residues within 4Å: Chain C: A.45 Ligands: MC3.34 Ligand excluded by PLIP MC3.34: 6 residues within 4Å: Chain C: G.41, M.44, A.45, F.52 Ligands: MC3.33, MC3.37 Ligand excluded by PLIP MC3.35: 4 residues within 4Å: Chain C: R.34, L.37, C.38 Chain E: F.14 Ligand excluded by PLIP MC3.36: 4 residues within 4Å: Chain C: D.270, L.271, C.272 Ligands: MC3.5 Ligand excluded by PLIP MC3.37: 1 residues within 4Å: Ligands: MC3.34 Ligand excluded by PLIP MC3.40: 8 residues within 4Å: Chain D: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.41 Ligand excluded by PLIP MC3.41: 8 residues within 4Å: Chain D: L.21, L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.40, MC3.49 Ligand excluded by PLIP MC3.42: 4 residues within 4Å: Chain D: Y.61, L.65 Ligands: MC3.23, DU0.39 Ligand excluded by PLIP MC3.43: 3 residues within 4Å: Chain D: A.45, Q.58 Ligands: DU0.39 Ligand excluded by PLIP MC3.44: 2 residues within 4Å: Chain D: A.45 Ligands: MC3.45 Ligand excluded by PLIP MC3.45: 6 residues within 4Å: Chain D: G.41, M.44, A.45, F.52 Ligands: MC3.44, MC3.48 Ligand excluded by PLIP MC3.46: 4 residues within 4Å: Chain B: F.14 Chain D: R.34, L.37, C.38 Ligand excluded by PLIP MC3.47: 4 residues within 4Å: Chain D: D.270, L.271, C.272 Ligands: MC3.55 Ligand excluded by PLIP MC3.48: 1 residues within 4Å: Ligands: MC3.45 Ligand excluded by PLIP MC3.49: 16 residues within 4Å: Chain D: F.14, G.15, S.18, Q.19, L.21, L.22 Chain E: E.35, C.38, F.39, F.42, Y.245, S.246, F.248, L.249, L.252 Ligands: MC3.41 Ligand excluded by PLIP MC3.50: 16 residues within 4Å: Chain C: E.35, C.38, F.39, F.42, Y.245, S.246, F.248, L.249, L.252 Chain E: F.14, G.15, S.18, Q.19, L.21, L.22 Ligands: MC3.54 Ligand excluded by PLIP MC3.53: 8 residues within 4Å: Chain E: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.54 Ligand excluded by PLIP MC3.54: 8 residues within 4Å: Chain E: L.21, L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.50, MC3.53 Ligand excluded by PLIP MC3.55: 4 residues within 4Å: Chain E: Y.61, L.65 Ligands: MC3.47, DU0.52 Ligand excluded by PLIP MC3.56: 3 residues within 4Å: Chain E: A.45, Q.58 Ligands: DU0.52 Ligand excluded by PLIP MC3.57: 2 residues within 4Å: Chain E: A.45 Ligands: MC3.58 Ligand excluded by PLIP MC3.58: 6 residues within 4Å: Chain E: G.41, M.44, A.45, F.52 Ligands: MC3.57, MC3.61 Ligand excluded by PLIP MC3.59: 4 residues within 4Å: Chain D: F.14 Chain E: R.34, L.37, C.38 Ligand excluded by PLIP MC3.60: 4 residues within 4Å: Chain E: D.270, L.271, C.272 Ligands: MC3.31 Ligand excluded by PLIP MC3.61: 1 residues within 4Å: Ligands: MC3.58 Ligand excluded by PLIP

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

CL.13: 0 residues within 4Å: (No contacts) 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-2: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
C

E
D

Membrane

We predict this structure to be a membrane protein.
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Bestrophin-2

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