SMTL ID : 8d1f.1

hBest2 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: 8 residues within 4Å: Chain A: Q.293, N.296, P.297, G.299, D.301, D.304 Chain D: A.10, N.11 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:A.10, A:N.296, A:D.301, A:D.304, H2O.1 CA.13: 8 residues within 4Å: Chain B: Q.293, N.296, P.297, G.299, D.301, D.304 Chain C: A.10, N.11 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:N.296, B:D.301, B:D.304, C:A.10, H2O.6 CA.25: 8 residues within 4Å: Chain C: Q.293, N.296, P.297, G.299, D.301, D.304 Chain E: A.10, N.11 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: C:N.296, C:D.301, C:D.304, E:A.10, H2O.11 CA.38: 8 residues within 4Å: Chain B: A.10, N.11 Chain D: Q.293, N.296, P.297, G.299, D.301, D.304 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:N.296, D:D.301, D:D.304, B:A.10, H2O.16 CA.50: 8 residues within 4Å: Chain A: A.10, N.11 Chain E: Q.293, N.296, P.297, G.299, D.301, D.304 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: E:N.296, E:D.301, E:D.304, A:A.10, H2O.21

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: 14 residues within 4Å: Chain A: F.42, L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.3, MC3.6, MC3.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.65, A:L.252 DU0.14: 14 residues within 4Å: Chain B: F.42, L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.15, MC3.18, MC3.19 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.65, B:L.252 DU0.26: 14 residues within 4Å: Chain C: F.42, L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.27, MC3.30, MC3.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.65, C:L.252 DU0.39: 14 residues within 4Å: Chain D: F.42, L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.40, MC3.43, MC3.44 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.65, D:L.252 DU0.51: 14 residues within 4Å: Chain E: F.42, L.46, L.54, G.57, Q.58, Y.61, F.62, L.65, L.249, L.252, I.253 Ligands: MC3.52, MC3.55, MC3.56 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.65, E:L.252

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

MC3.3: 20 residues within 4Å: Chain A: E.35, C.38, F.39, F.42, I.242, Y.245, S.246, F.248, L.249, L.252, F.281 Chain D: F.14, G.15, S.18, Q.19, L.21, L.22, L.279 Ligands: DU0.2, MC3.42 Ligand excluded by PLIP MC3.4: 8 residues within 4Å: Chain A: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.5 Ligand excluded by PLIP MC3.5: 11 residues within 4Å: Chain A: L.21, L.22, L.23, W.24, R.25, Y.29, W.33, L.36, F.282 Ligands: MC3.4, MC3.52 Ligand excluded by PLIP MC3.6: 9 residues within 4Å: Chain A: Y.61, L.65, L.249, I.253 Chain D: L.271, I.275, F.276 Ligands: DU0.2, MC3.48 Ligand excluded by PLIP MC3.7: 9 residues within 4Å: Chain A: F.42, A.45, L.46, A.49, V.53, L.54, Q.58 Ligands: DU0.2, MC3.8 Ligand excluded by PLIP MC3.8: 6 residues within 4Å: Chain A: A.45, A.48, F.52, V.53 Ligands: MC3.7, MC3.9 Ligand excluded by PLIP MC3.9: 7 residues within 4Å: Chain A: G.41, M.44, A.45, A.48, F.52 Ligands: MC3.8, MC3.12 Ligand excluded by PLIP MC3.10: 8 residues within 4Å: Chain A: W.33, R.34, L.37, C.38, G.41 Chain D: R.13, F.14, G.15 Ligand excluded by PLIP MC3.11: 7 residues within 4Å: Chain A: D.270, L.271, C.272, V.273, I.275 Chain E: Y.61 Ligands: MC3.55 Ligand excluded by PLIP MC3.12: 7 residues within 4Å: Chain A: M.44, S.47, A.48, R.51, F.52, C.272 Ligands: MC3.9 Ligand excluded by PLIP MC3.15: 20 residues within 4Å: Chain B: E.35, C.38, F.39, F.42, I.242, Y.245, S.246, F.248, L.249, L.252, F.281 Chain C: F.14, G.15, S.18, Q.19, L.21, L.22, L.279 Ligands: DU0.14, MC3.29 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: 11 residues within 4Å: Chain B: L.21, L.22, L.23, W.24, R.25, Y.29, W.33, L.36, F.282 Ligands: MC3.16, MC3.40 Ligand excluded by PLIP MC3.18: 9 residues within 4Å: Chain B: Y.61, L.65, L.249, I.253 Chain C: L.271, I.275, F.276 Ligands: DU0.14, MC3.35 Ligand excluded by PLIP MC3.19: 9 residues within 4Å: Chain B: F.42, A.45, L.46, A.49, V.53, L.54, Q.58 Ligands: DU0.14, MC3.20 Ligand excluded by PLIP MC3.20: 6 residues within 4Å: Chain B: A.45, A.48, F.52, V.53 Ligands: MC3.19, MC3.21 Ligand excluded by PLIP MC3.21: 7 residues within 4Å: Chain B: G.41, M.44, A.45, A.48, F.52 Ligands: MC3.20, MC3.23 Ligand excluded by PLIP MC3.22: 7 residues within 4Å: Chain B: D.270, L.271, C.272, V.273, I.275 Chain D: Y.61 Ligands: MC3.43 Ligand excluded by PLIP MC3.23: 7 residues within 4Å: Chain B: M.44, S.47, A.48, R.51, F.52, C.272 Ligands: MC3.21 Ligand excluded by PLIP MC3.24: 8 residues within 4Å: Chain B: W.33, R.34, L.37, C.38, G.41 Chain C: R.13, F.14, G.15 Ligand excluded by PLIP MC3.27: 20 residues within 4Å: Chain C: E.35, C.38, F.39, F.42, I.242, Y.245, S.246, F.248, L.249, L.252, F.281 Chain E: F.14, G.15, S.18, Q.19, L.21, L.22, L.279 Ligands: DU0.26, MC3.54 Ligand excluded by PLIP MC3.28: 8 residues within 4Å: Chain C: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.29 Ligand excluded by PLIP MC3.29: 11 residues within 4Å: Chain C: L.21, L.22, L.23, W.24, R.25, Y.29, W.33, L.36, F.282 Ligands: MC3.15, MC3.28 Ligand excluded by PLIP MC3.30: 9 residues within 4Å: Chain C: Y.61, L.65, L.249, I.253 Chain E: L.271, I.275, F.276 Ligands: DU0.26, MC3.60 Ligand excluded by PLIP MC3.31: 9 residues within 4Å: Chain C: F.42, A.45, L.46, A.49, V.53, L.54, Q.58 Ligands: DU0.26, MC3.32 Ligand excluded by PLIP MC3.32: 6 residues within 4Å: Chain C: A.45, A.48, F.52, V.53 Ligands: MC3.31, MC3.33 Ligand excluded by PLIP MC3.33: 7 residues within 4Å: Chain C: G.41, M.44, A.45, A.48, F.52 Ligands: MC3.32, MC3.36 Ligand excluded by PLIP MC3.34: 8 residues within 4Å: Chain C: W.33, R.34, L.37, C.38, G.41 Chain E: R.13, F.14, G.15 Ligand excluded by PLIP MC3.35: 7 residues within 4Å: Chain B: Y.61 Chain C: D.270, L.271, C.272, V.273, I.275 Ligands: MC3.18 Ligand excluded by PLIP MC3.36: 7 residues within 4Å: Chain C: M.44, S.47, A.48, R.51, F.52, C.272 Ligands: MC3.33 Ligand excluded by PLIP MC3.40: 20 residues within 4Å: Chain B: F.14, G.15, S.18, Q.19, L.21, L.22, L.279 Chain D: E.35, C.38, F.39, F.42, I.242, Y.245, S.246, F.248, L.249, L.252, F.281 Ligands: MC3.17, DU0.39 Ligand excluded by PLIP MC3.41: 8 residues within 4Å: Chain D: W.24, W.33, R.34, L.36, L.37, L.40, L.278 Ligands: MC3.42 Ligand excluded by PLIP MC3.42: 11 residues within 4Å: Chain D: L.21, L.22, L.23, W.24, R.25, Y.29, W.33, L.36, F.282 Ligands: MC3.3, MC3.41 Ligand excluded by PLIP MC3.43: 9 residues within 4Å: Chain B: L.271, I.275, F.276 Chain D: Y.61, L.65, L.249, I.253 Ligands: MC3.22, DU0.39 Ligand excluded by PLIP MC3.44: 9 residues within 4Å: Chain D: F.42, A.45, L.46, A.49, V.53, L.54, Q.58 Ligands: DU0.39, MC3.45 Ligand excluded by PLIP MC3.45: 6 residues within 4Å: Chain D: A.45, A.48, F.52, V.53 Ligands: MC3.44, MC3.46 Ligand excluded by PLIP MC3.46: 7 residues within 4Å: Chain D: G.41, M.44, A.45, A.48, F.52 Ligands: MC3.45, MC3.49 Ligand excluded by PLIP MC3.47: 8 residues within 4Å: Chain B: R.13, F.14, G.15 Chain D: W.33, R.34, L.37, C.38, G.41 Ligand excluded by PLIP MC3.48: 7 residues within 4Å: Chain A: Y.61 Chain D: D.270, L.271, C.272, V.273, I.275 Ligands: MC3.6 Ligand excluded by PLIP MC3.49: 7 residues within 4Å: Chain D: M.44, S.47, A.48, R.51, F.52, C.272 Ligands: MC3.46 Ligand excluded by PLIP MC3.52: 20 residues within 4Å: Chain A: F.14, G.15, S.18, Q.19, L.21, L.22, L.279 Chain E: E.35, C.38, F.39, F.42, I.242, Y.245, S.246, F.248, L.249, L.252, F.281 Ligands: MC3.5, DU0.51 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: 11 residues within 4Å: Chain E: L.21, L.22, L.23, W.24, R.25, Y.29, W.33, L.36, F.282 Ligands: MC3.27, MC3.53 Ligand excluded by PLIP MC3.55: 9 residues within 4Å: Chain A: L.271, I.275, F.276 Chain E: Y.61, L.65, L.249, I.253 Ligands: MC3.11, DU0.51 Ligand excluded by PLIP MC3.56: 9 residues within 4Å: Chain E: F.42, A.45, L.46, A.49, V.53, L.54, Q.58 Ligands: DU0.51, MC3.57 Ligand excluded by PLIP MC3.57: 6 residues within 4Å: Chain E: A.45, A.48, F.52, V.53 Ligands: MC3.56, MC3.58 Ligand excluded by PLIP MC3.58: 7 residues within 4Å: Chain E: G.41, M.44, A.45, A.48, F.52 Ligands: MC3.57, MC3.61 Ligand excluded by PLIP MC3.59: 8 residues within 4Å: Chain A: R.13, F.14, G.15 Chain E: W.33, R.34, L.37, C.38, G.41 Ligand excluded by PLIP MC3.60: 7 residues within 4Å: Chain C: Y.61 Chain E: D.270, L.271, C.272, V.273, I.275 Ligands: MC3.30 Ligand excluded by PLIP MC3.61: 7 residues within 4Å: Chain E: M.44, S.47, A.48, R.51, F.52, C.272 Ligands: MC3.58 Ligand excluded by PLIP

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

CL.37: 5 residues within 4Å: Chain A: K.208 Chain B: K.208 Chain C: K.208 Chain D: K.208 Chain E: K.208 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
C

B
E

C
A

D
D

E
B

Membrane

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

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