SMTL ID : 4rdq.1

Calcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments, chloride and calcium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-5-5-5-mer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: A.145, G.298, E.299, D.300, D.303, F.304, E.305, T.306, N.307 Chain E: Y.353, R.355 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:T.306, A:N.307, A:N.307, E:R.355, E:R.355 GOL.8: 11 residues within 4Å: Chain A: Y.353, R.355 Chain B: A.145, G.298, E.299, D.300, D.303, F.304, E.305, T.306, N.307 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.305, B:T.306, B:N.307, B:N.307, A:R.355, A:R.355 GOL.15: 11 residues within 4Å: Chain B: Y.353, R.355 Chain C: A.145, G.298, E.299, D.300, D.303, F.304, E.305, T.306, N.307 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.355, B:R.355, C:E.305, C:T.306, C:N.307, C:N.307 GOL.23: 11 residues within 4Å: Chain C: Y.353, R.355 Chain D: A.145, G.298, E.299, D.300, D.303, F.304, E.305, T.306, N.307 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.300, D:T.306, D:T.306, D:N.307, D:N.307, C:R.355, C:R.355 GOL.29: 11 residues within 4Å: Chain D: Y.353, R.355 Chain E: A.145, G.298, E.299, 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

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

CL.2: 5 residues within 4Å: Chain A: P.273, F.275, T.276 Chain B: Y.67, Y.71 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: E.73, L.74, I.75 Ligand excluded by PLIP CL.5: 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, I.75 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain C: S.218 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain C: P.273, F.275, T.276 Chain D: Y.67, Y.71 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: E.73, L.74, I.75 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain D: R.217, S.218 Ligand excluded by PLIP CL.26: 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.27: 3 residues within 4Å: Chain D: E.73, L.74, I.75 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain E: S.218 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain A: Y.67, Y.71 Chain E: P.273, F.275, T.276 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain E: E.73, L.74, I.75 Ligand excluded by PLIP

5 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.16: 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.24: 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.30: 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

5 x K: POTASSIUM ION(Non-covalent)

K.6: 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.13: 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.20: 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.21: 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.34: 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 C6N: 6-cyclohexyl-2-(4-cyclohexylbutyl)-2-({[4-O-(alpha-D-glucopyranosyl)-beta-D-glucopyranosyl]oxy}methyl)hexyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside(Non-covalent)

C6N.7: 10 residues within 4Å: Chain A: R.7, D.10, R.12, G.14, T.15, Q.18, L.21 Chain B: Y.244 Chain I: K.55, E.57 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.21, A:L.21 Hydrogen bonds: A:D.10, A:D.10, A:T.15, A:Q.18 C6N.14: 11 residues within 4Å: Chain B: R.7, D.10, R.12, G.14, T.15, S.17, Q.18, L.21 Chain C: Y.244 Chain K: K.55, E.57 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.21, B:L.21 Hydrogen bonds: B:D.10, B:D.10, B:T.15, B:Q.18 C6N.22: 11 residues within 4Å: Chain C: R.7, D.10, R.12, G.14, T.15, S.17, Q.18, L.21 Chain D: Y.244 Chain M: K.55, E.57 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain M Hydrophobic interactions: C:L.21, C:L.21 Hydrogen bonds: C:D.10, C:D.10, C:T.15, C:Q.18, M:E.57 C6N.28: 10 residues within 4Å: Chain D: R.7, D.10, R.12, G.14, T.15, Q.18, L.21 Chain E: Y.244 Chain O: K.55, E.57 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain O Hydrophobic interactions: D:L.21, D:L.21 Hydrogen bonds: D:D.10, D:T.15, D:Q.18, O:E.57 C6N.35: 9 residues within 4Å: Chain A: Y.244 Chain E: R.7, D.10, R.12, G.14, T.15, Q.18, L.21 Chain G: K.55 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.21, E:L.21 Hydrogen bonds: E:D.10, E:T.15, E:Q.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kane Dickson, V. et al., Structure and insights into the function of a Ca(2+)-activated Cl(-) channel. Nature (2014)

Release Date

2014-10-22

Peptides

Bestrophin-1: ABCDE
Fab antibody fragment, light chain: FHJLN
Fab antibody fragment, heavy chain: 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

Fab antibody fragment, light chain

Fab antibody fragment, heavy chain

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