SMTL ID : 8d1e.1

hBest2 1uM 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.1 CA.13: 5 residues within 4Å: Chain A: A.10 Chain B: Q.293, N.296, D.301, D.304 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:N.296, B:D.301, B:D.304, A:A.10, H2O.6 CA.26: 5 residues within 4Å: Chain C: Q.293, N.296, D.301, D.304 Chain E: A.10 5 PLIP interactions: 1 interactions with chain E, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:A.10, C:N.296, C:D.301, C:D.304, H2O.11 CA.37: 5 residues within 4Å: Chain B: A.10 Chain D: Q.293, N.296, 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.15 CA.51: 5 residues within 4Å: Chain D: A.10 Chain E: Q.293, N.296, D.301, D.304 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:N.296, E:D.301, E:D.304, D:A.10, H2O.20

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

MC3.2: 13 residues within 4Å: Chain A: E.35, C.38, Y.245, S.246, F.248, L.249 Chain C: F.14, G.15, S.18, L.21, L.22, L.279 Ligands: MC3.29 Ligand excluded by PLIP MC3.3: 6 residues within 4Å: Chain A: W.24, W.33, R.34, L.36, L.37 Ligands: MC3.4 Ligand excluded by PLIP MC3.4: 9 residues within 4Å: Chain A: L.21, L.22, L.23, W.24, R.25, Y.29, F.282 Ligands: MC3.3, MC3.14 Ligand excluded by PLIP MC3.5: 4 residues within 4Å: Chain A: Y.61, L.65 Ligands: DU0.11, MC3.34 Ligand excluded by PLIP MC3.6: 2 residues within 4Å: Chain A: F.42 Ligands: DU0.11 Ligand excluded by PLIP MC3.7: 2 residues within 4Å: Chain A: V.53 Ligands: MC3.8 Ligand excluded by PLIP MC3.8: 4 residues within 4Å: Chain A: M.44, F.52 Ligands: MC3.7, MC3.10 Ligand excluded by PLIP MC3.9: 3 residues within 4Å: Chain A: L.271, I.275 Ligands: MC3.17 Ligand excluded by PLIP MC3.10: 2 residues within 4Å: Chain A: C.272 Ligands: MC3.8 Ligand excluded by PLIP MC3.12: 4 residues within 4Å: Chain A: R.13, F.14 Chain B: R.34, C.38 Ligand excluded by PLIP MC3.14: 13 residues within 4Å: Chain A: F.14, G.15, S.18, L.21, L.22, L.279 Chain B: E.35, C.38, Y.245, S.246, F.248, L.249 Ligands: MC3.4 Ligand excluded by PLIP MC3.15: 6 residues within 4Å: Chain B: W.24, W.33, R.34, L.36, L.37 Ligands: MC3.16 Ligand excluded by PLIP MC3.16: 9 residues within 4Å: Chain B: L.21, L.22, L.23, W.24, R.25, Y.29, F.282 Ligands: MC3.15, MC3.38 Ligand excluded by PLIP MC3.17: 4 residues within 4Å: Chain B: Y.61, L.65 Ligands: MC3.9, DU0.23 Ligand excluded by PLIP MC3.18: 2 residues within 4Å: Chain B: F.42 Ligands: DU0.23 Ligand excluded by PLIP MC3.19: 2 residues within 4Å: Chain B: V.53 Ligands: MC3.20 Ligand excluded by PLIP MC3.20: 4 residues within 4Å: Chain B: M.44, F.52 Ligands: MC3.19, MC3.22 Ligand excluded by PLIP MC3.21: 3 residues within 4Å: Chain B: L.271, I.275 Ligands: MC3.41 Ligand excluded by PLIP MC3.22: 2 residues within 4Å: Chain B: C.272 Ligands: MC3.20 Ligand excluded by PLIP MC3.24: 4 residues within 4Å: Chain B: R.13, F.14 Chain D: R.34, C.38 Ligand excluded by PLIP MC3.25: 4 residues within 4Å: Chain A: R.34, C.38 Chain C: R.13, F.14 Ligand excluded by PLIP MC3.27: 13 residues within 4Å: Chain C: E.35, C.38, Y.245, S.246, F.248, L.249 Chain E: F.14, G.15, S.18, L.21, L.22, L.279 Ligands: MC3.54 Ligand excluded by PLIP MC3.28: 6 residues within 4Å: Chain C: W.24, W.33, R.34, L.36, L.37 Ligands: MC3.29 Ligand excluded by PLIP MC3.29: 9 residues within 4Å: Chain C: L.21, L.22, L.23, W.24, R.25, Y.29, F.282 Ligands: MC3.2, MC3.28 Ligand excluded by PLIP MC3.30: 4 residues within 4Å: Chain C: Y.61, L.65 Ligands: DU0.36, MC3.59 Ligand excluded by PLIP MC3.31: 2 residues within 4Å: Chain C: F.42 Ligands: DU0.36 Ligand excluded by PLIP MC3.32: 2 residues within 4Å: Chain C: V.53 Ligands: MC3.33 Ligand excluded by PLIP MC3.33: 4 residues within 4Å: Chain C: M.44, F.52 Ligands: MC3.32, MC3.35 Ligand excluded by PLIP MC3.34: 3 residues within 4Å: Chain C: L.271, I.275 Ligands: MC3.5 Ligand excluded by PLIP MC3.35: 2 residues within 4Å: Chain C: C.272 Ligands: MC3.33 Ligand excluded by PLIP MC3.38: 13 residues within 4Å: Chain B: F.14, G.15, S.18, L.21, L.22, L.279 Chain D: E.35, C.38, Y.245, S.246, F.248, L.249 Ligands: MC3.16 Ligand excluded by PLIP MC3.39: 6 residues within 4Å: Chain D: W.24, W.33, R.34, L.36, L.37 Ligands: MC3.40 Ligand excluded by PLIP MC3.40: 9 residues within 4Å: Chain D: L.21, L.22, L.23, W.24, R.25, Y.29, F.282 Ligands: MC3.39, MC3.52 Ligand excluded by PLIP MC3.41: 4 residues within 4Å: Chain D: Y.61, L.65 Ligands: MC3.21, DU0.47 Ligand excluded by PLIP MC3.42: 2 residues within 4Å: Chain D: F.42 Ligands: DU0.47 Ligand excluded by PLIP MC3.43: 2 residues within 4Å: Chain D: V.53 Ligands: MC3.44 Ligand excluded by PLIP MC3.44: 4 residues within 4Å: Chain D: M.44, F.52 Ligands: MC3.43, MC3.46 Ligand excluded by PLIP MC3.45: 3 residues within 4Å: Chain D: L.271, I.275 Ligands: MC3.55 Ligand excluded by PLIP MC3.46: 2 residues within 4Å: Chain D: C.272 Ligands: MC3.44 Ligand excluded by PLIP MC3.48: 4 residues within 4Å: Chain D: R.13, F.14 Chain E: R.34, C.38 Ligand excluded by PLIP MC3.50: 4 residues within 4Å: Chain C: R.34, C.38 Chain E: R.13, F.14 Ligand excluded by PLIP MC3.52: 13 residues within 4Å: Chain D: F.14, G.15, S.18, L.21, L.22, L.279 Chain E: E.35, C.38, Y.245, S.246, F.248, L.249 Ligands: MC3.40 Ligand excluded by PLIP MC3.53: 6 residues within 4Å: Chain E: W.24, W.33, R.34, L.36, L.37 Ligands: MC3.54 Ligand excluded by PLIP MC3.54: 9 residues within 4Å: Chain E: L.21, L.22, L.23, W.24, R.25, Y.29, F.282 Ligands: MC3.27, MC3.53 Ligand excluded by PLIP MC3.55: 4 residues within 4Å: Chain E: Y.61, L.65 Ligands: MC3.45, DU0.61 Ligand excluded by PLIP MC3.56: 2 residues within 4Å: Chain E: F.42 Ligands: DU0.61 Ligand excluded by PLIP MC3.57: 2 residues within 4Å: Chain E: V.53 Ligands: MC3.58 Ligand excluded by PLIP MC3.58: 4 residues within 4Å: Chain E: M.44, F.52 Ligands: MC3.57, MC3.60 Ligand excluded by PLIP MC3.59: 3 residues within 4Å: Chain E: L.271, I.275 Ligands: MC3.30 Ligand excluded by PLIP MC3.60: 2 residues within 4Å: Chain E: C.272 Ligands: MC3.58 Ligand excluded by PLIP

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)

DU0.11: 13 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: MC3.5, MC3.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.46, A:L.54, A:L.252 DU0.23: 13 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: MC3.17, MC3.18 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.46, B:L.54, B:L.252 DU0.36: 13 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: MC3.30, MC3.31 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.46, C:L.54, C:L.252 DU0.47: 13 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: MC3.41, MC3.42 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.46, D:L.54, D:L.252 DU0.61: 13 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: MC3.55, MC3.56 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.46, E:L.54, E:L.252

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

CL.49: 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
D

B
E

C
C

D
A

E
B

Membrane

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

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