SMTL ID : 5kmf.1

Structure of CavAb in complex with nimodipine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-tetramer

Ligands

1 x 6U9: nimodipine(Non-covalent)

6U9.1: 7 residues within 4Å: Chain A: T.180, G.182, E.183, F.185, Y.186 Chain C: Y.213, I.217 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.185, C:Y.213, C:Y.213, C:I.217 Hydrogen bonds: A:G.182

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

MC3.2: 5 residues within 4Å: Chain A: L.194, F.221, T.224 Chain B: M.192, T.193 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.194, A:F.221, A:T.224 MC3.3: 2 residues within 4Å: Chain A: F.170, Y.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.208 MC3.4: 5 residues within 4Å: Chain A: S.52, K.53 Chain C: T.180, L.181, G.182 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.53, C:L.181, C:G.182 MC3.5: 5 residues within 4Å: Chain A: L.194 Chain B: T.193, L.194 Chain C: L.194 Ligands: CA.17 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.194, C:L.194 MC3.6: 10 residues within 4Å: Chain A: Y.213, F.221 Chain B: M.155, T.156, F.159, G.182, E.183, F.185, Y.186, F.189 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:M.155, B:F.159, B:F.185, B:F.189, B:F.189, A:F.221 Hydrogen bonds: A:Y.213 MC3.7: 6 residues within 4Å: Chain B: L.169, F.170, Y.209, Y.211, A.212 Chain D: I.115 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.211 MC3.9: 2 residues within 4Å: Chain A: M.192 Chain C: T.224 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.224 MC3.10: 1 residues within 4Å: Chain C: Y.209 No protein-ligand interaction detected (PLIP) MC3.11: 2 residues within 4Å: Chain C: I.115 Chain D: Y.209 No protein-ligand interaction detected (PLIP) MC3.12: 4 residues within 4Å: Chain C: G.48, T.51, S.52 Chain D: T.180 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.52 MC3.13: 3 residues within 4Å: Chain B: L.194 Chain D: M.192, M.227 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.194 MC3.14: 8 residues within 4Å: Chain C: F.159, T.180, G.182, E.183, F.189 Chain D: Y.213, I.217, F.221 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.159, C:F.189, D:F.221 Hydrogen bonds: C:T.180, D:Y.213 MC3.15: 8 residues within 4Å: Chain B: Y.213, F.221 Chain D: F.159, G.182, E.183, F.185, Y.186, F.189 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.221, D:F.159, D:F.189 MC3.16: 3 residues within 4Å: Chain B: T.180 Chain D: S.52, T.54 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.52, D:T.54, D:T.54, B:T.180

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: D.195, D.196 Chain C: D.196 No protein-ligand interaction detected (PLIP) CA.17: 3 residues within 4Å: Chain D: D.195, D.196 Ligands: MC3.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, L. et al., Structural basis for inhibition of a voltage-gated Ca(2+) channel by Ca(2+) antagonist drugs. Nature (2016)

Release Date

2016-08-31

Peptides

Ion transport protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Ion transport protein

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