SMTL ID : 5t5n.1

Calcium-activated chloride channel bestrophin-1 (BEST1), triple mutant: I76A, F80A, F84A; in complex with an Fab antibody fragment, chloride, and calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-5-5-5-mer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: P.273, V.274, F.275, T.276 Chain B: Y.67, Y.71 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: E.73, L.74, A.75 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain A: S.218 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.217, S.218 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: P.273, V.274, F.275, T.276 Chain C: Y.67, Y.71 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: E.73, L.74, A.75 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: R.217, S.218 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain C: P.273, V.274, F.275, T.276 Chain D: Y.67, Y.71 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: E.73, L.74, A.75 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: R.217, S.218 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain D: P.273, V.274, F.275, T.276 Chain E: Y.67, Y.71 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: E.73, L.74, A.75 Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain E: S.218 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain A: Y.67, Y.71 Chain E: P.273, F.275, T.276 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain E: E.73, L.74, A.75 Ligand excluded by PLIP

5 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: L.13, S.17 Chain B: E.34, Y.244, E.291 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:Y.244, A:L.13 K.7: 5 residues within 4Å: Chain A: E.34, Y.244, E.291 Chain E: L.13, S.17 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Metal complexes: E:L.13, A:Y.244 K.16: 5 residues within 4Å: Chain B: L.13, S.17 Chain C: E.34, Y.244, E.291 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:L.13, C:Y.244 K.19: 5 residues within 4Å: Chain C: L.13, S.17 Chain D: E.34, Y.244, E.291 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:Y.244, C:L.13 K.28: 5 residues within 4Å: Chain D: L.13, S.17 Chain E: E.34, Y.244, E.291 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Metal complexes: E:Y.244, D:L.13

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: A.145, G.298, D.300, D.303, F.304, E.305, T.306, N.307 Chain E: Y.353, R.355 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:D.300, A:T.306, A:N.307, A:N.307, E:R.355, E:R.355 GOL.8: 10 residues within 4Å: Chain A: Y.353, R.355 Chain B: A.145, G.298, D.300, D.303, F.304, E.305, T.306, N.307 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.300, B:E.305, B:T.306, B:N.307, B:N.307, A:R.355, A:R.355 GOL.13: 10 residues within 4Å: Chain B: Y.353, R.355 Chain C: A.145, G.298, D.300, D.303, F.304, E.305, T.306, N.307 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.305, C:T.306, C:T.306, C:N.307, C:N.307, B:R.355, B:R.355 GOL.20: 10 residues within 4Å: Chain C: Y.353, R.355 Chain D: A.145, G.298, D.300, D.303, F.304, E.305, T.306, N.307 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.300, D:E.305, D:T.306, D:T.306, D:N.307, D:N.307, C:R.355, C:R.355 GOL.25: 10 residues within 4Å: Chain D: Y.353, R.355 Chain E: A.145, G.298, D.300, D.303, F.304, E.305, T.306, N.307 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:R.355, D:R.355, E:D.300, E:T.306, E:T.306, E:N.307, E:N.307

5 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: Q.292, N.295, D.300, D.303 Chain E: A.9 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: A:N.295, A:D.300, A:D.303, E:A.9, H2O.1 CA.9: 5 residues within 4Å: Chain A: A.9 Chain B: Q.292, N.295, D.300, D.303 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:N.295, B:D.300, B:D.303, A:A.9, H2O.1 CA.14: 5 residues within 4Å: Chain B: A.9 Chain C: Q.292, N.295, D.300, D.303 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:A.9, C:N.295, C:D.300, C:D.303, H2O.1 CA.21: 5 residues within 4Å: Chain C: A.9 Chain D: Q.292, N.295, D.300, D.303 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:N.295, D:D.300, D:D.303, C:A.9, H2O.1 CA.26: 5 residues within 4Å: Chain D: A.9 Chain E: Q.292, N.295, D.300, D.303 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:N.295, E:D.300, E:D.303, D:A.9, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vaisey, G. et al., Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-11-30

Peptides

bestrophin-1 (BEST1): ABCDE
Fab antibody fragment, light chain (10D10): FHJLN
Fab antibody fragment, heavy chain (10D10): GIKMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

H
H

J
J

L
L

N
N

G
G

I
I

K
K

M
M

O
O

Membrane

We predict this structure to be a membrane protein.
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bestrophin-1 (BEST1)

Fab antibody fragment, light chain (10D10)

Fab antibody fragment, heavy chain (10D10)

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