SMTL ID : 8d1h.1

hBest2 Ca2+-unbound closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

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

MC3.1: 3 residues within 4Å: Chain A: W.33, L.37 Ligands: MC3.2 Ligand excluded by PLIP MC3.2: 6 residues within 4Å: Chain A: L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.1 Ligand excluded by PLIP MC3.3: 3 residues within 4Å: Chain A: Y.61, L.65 Ligands: DU0.8 Ligand excluded by PLIP MC3.4: 2 residues within 4Å: Chain A: Q.58 Ligands: DU0.8 Ligand excluded by PLIP MC3.5: 3 residues within 4Å: Chain A: A.48, F.52, V.53 Ligand excluded by PLIP MC3.6: 1 residues within 4Å: Chain A: F.52 Ligand excluded by PLIP MC3.7: 3 residues within 4Å: Chain A: M.44, R.51, C.272 Ligand excluded by PLIP MC3.9: 7 residues within 4Å: Chain A: F.14, S.18 Chain C: F.39, Y.245, S.246, F.248 Ligands: MC3.10 Ligand excluded by PLIP MC3.10: 5 residues within 4Å: Chain A: R.13, F.14 Chain C: R.34, C.38 Ligands: MC3.9 Ligand excluded by PLIP MC3.11: 3 residues within 4Å: Chain B: W.33, L.37 Ligands: MC3.12 Ligand excluded by PLIP MC3.12: 6 residues within 4Å: Chain B: L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.11 Ligand excluded by PLIP MC3.13: 3 residues within 4Å: Chain B: Y.61, L.65 Ligands: DU0.18 Ligand excluded by PLIP MC3.14: 2 residues within 4Å: Chain B: Q.58 Ligands: DU0.18 Ligand excluded by PLIP MC3.15: 3 residues within 4Å: Chain B: A.48, F.52, V.53 Ligand excluded by PLIP MC3.16: 1 residues within 4Å: Chain B: F.52 Ligand excluded by PLIP MC3.17: 3 residues within 4Å: Chain B: M.44, R.51, C.272 Ligand excluded by PLIP MC3.19: 7 residues within 4Å: Chain B: F.14, S.18 Chain D: F.39, Y.245, S.246, F.248 Ligands: MC3.20 Ligand excluded by PLIP MC3.20: 5 residues within 4Å: Chain B: R.13, F.14 Chain D: R.34, C.38 Ligands: MC3.19 Ligand excluded by PLIP MC3.21: 7 residues within 4Å: Chain B: F.39, Y.245, S.246, F.248 Chain C: F.14, S.18 Ligands: MC3.22 Ligand excluded by PLIP MC3.22: 5 residues within 4Å: Chain B: R.34, C.38 Chain C: R.13, F.14 Ligands: MC3.21 Ligand excluded by PLIP MC3.23: 3 residues within 4Å: Chain C: W.33, L.37 Ligands: MC3.24 Ligand excluded by PLIP MC3.24: 6 residues within 4Å: Chain C: L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.23 Ligand excluded by PLIP MC3.25: 3 residues within 4Å: Chain C: Y.61, L.65 Ligands: DU0.30 Ligand excluded by PLIP MC3.26: 2 residues within 4Å: Chain C: Q.58 Ligands: DU0.30 Ligand excluded by PLIP MC3.27: 3 residues within 4Å: Chain C: A.48, F.52, V.53 Ligand excluded by PLIP MC3.28: 1 residues within 4Å: Chain C: F.52 Ligand excluded by PLIP MC3.29: 3 residues within 4Å: Chain C: M.44, R.51, C.272 Ligand excluded by PLIP MC3.32: 3 residues within 4Å: Chain D: W.33, L.37 Ligands: MC3.33 Ligand excluded by PLIP MC3.33: 6 residues within 4Å: Chain D: L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.32 Ligand excluded by PLIP MC3.34: 3 residues within 4Å: Chain D: Y.61, L.65 Ligands: DU0.39 Ligand excluded by PLIP MC3.35: 2 residues within 4Å: Chain D: Q.58 Ligands: DU0.39 Ligand excluded by PLIP MC3.36: 3 residues within 4Å: Chain D: A.48, F.52, V.53 Ligand excluded by PLIP MC3.37: 1 residues within 4Å: Chain D: F.52 Ligand excluded by PLIP MC3.38: 3 residues within 4Å: Chain D: M.44, R.51, C.272 Ligand excluded by PLIP MC3.40: 7 residues within 4Å: Chain D: F.14, S.18 Chain E: F.39, Y.245, S.246, F.248 Ligands: MC3.41 Ligand excluded by PLIP MC3.41: 5 residues within 4Å: Chain D: R.13, F.14 Chain E: R.34, C.38 Ligands: MC3.40 Ligand excluded by PLIP MC3.42: 7 residues within 4Å: Chain A: F.39, Y.245, S.246, F.248 Chain E: F.14, S.18 Ligands: MC3.43 Ligand excluded by PLIP MC3.43: 5 residues within 4Å: Chain A: R.34, C.38 Chain E: R.13, F.14 Ligands: MC3.42 Ligand excluded by PLIP MC3.44: 3 residues within 4Å: Chain E: W.33, L.37 Ligands: MC3.45 Ligand excluded by PLIP MC3.45: 6 residues within 4Å: Chain E: L.22, L.23, W.24, R.25, Y.29 Ligands: MC3.44 Ligand excluded by PLIP MC3.46: 3 residues within 4Å: Chain E: Y.61, L.65 Ligands: DU0.51 Ligand excluded by PLIP MC3.47: 2 residues within 4Å: Chain E: Q.58 Ligands: DU0.51 Ligand excluded by PLIP MC3.48: 3 residues within 4Å: Chain E: A.48, F.52, V.53 Ligand excluded by PLIP MC3.49: 1 residues within 4Å: Chain E: F.52 Ligand excluded by PLIP MC3.50: 3 residues within 4Å: Chain E: M.44, R.51, C.272 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)

DU0.8: 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: MC3.3, MC3.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.54, A:Y.61, A:F.62, A:L.65, A:L.252 DU0.18: 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: MC3.13, MC3.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.54, B:Y.61, B:F.62, B:L.65, B:L.252 DU0.30: 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: MC3.25, MC3.26 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.54, C:Y.61, C:F.62, C:L.65, C:L.252 DU0.39: 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: MC3.34, MC3.35 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.54, D:Y.61, D:F.62, D:L.65, D:L.252 DU0.51: 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: MC3.46, MC3.47 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.54, E:Y.61, E:F.62, E:L.65, E:L.252

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

CL.31: 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
E

B
B

C
A

D
C

E
D

Membrane

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

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