SMTL ID : 6ke5.1

Structure of CavAb in complex with Diltiazem and Amlodipine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

3 x LPC: [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE(Non-covalent)

LPC.1: 8 residues within 4Å: Chain A: G.181, E.182, F.184, Y.185, F.188 Chain B: Y.212, I.216 Ligands: G3P.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.216, A:F.188 LPC.7: 9 residues within 4Å: Chain A: Y.212, I.216, F.220 Chain C: T.155, T.179, G.181, E.182, F.184, Y.185 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.220 LPC.11: 7 residues within 4Å: Chain C: Y.212 Chain D: T.155, G.181, E.182, F.184, Y.185, F.188 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.188

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.195 Chain C: D.195 Chain D: D.195 Ligands: CA.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.195 CA.9: 4 residues within 4Å: Chain C: T.192, L.193, D.194 Ligands: CA.12 No protein-ligand interaction detected (PLIP) CA.12: 7 residues within 4Å: Chain A: D.194 Chain B: D.194, D.195 Chain D: L.193, D.195 Ligands: CA.2, CA.9 No protein-ligand interaction detected (PLIP)

5 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.3: 4 residues within 4Å: Chain A: L.168, F.169, Y.208 Chain C: I.114 No protein-ligand interaction detected (PLIP) G3P.4: 3 residues within 4Å: Chain A: T.179, L.180 Ligands: LPC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.179 G3P.6: 6 residues within 4Å: Chain B: G.47, L.48, T.50, S.51 Chain D: T.179, L.180 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.47, B:S.51, B:S.51, B:S.51 G3P.10: 7 residues within 4Å: Chain C: L.168, F.169, Y.208, P.209, Y.210, A.211 Chain D: F.112 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.210, C:Y.210 G3P.13: 6 residues within 4Å: Chain B: E.113 Chain D: L.168, F.169, Y.208, Y.210, A.211 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:E.113, B:E.113, D:Y.210, D:Y.210

1 x 6UB: amlodipine(Non-covalent)

6UB.5: 5 residues within 4Å: Chain B: G.181, E.182, F.184, Y.185 Chain D: Y.212 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.184 Hydrogen bonds: B:Y.185

1 x D6C: [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate(Non-covalent)

D6C.8: 10 residues within 4Å: Chain C: T.192, L.193, F.220, T.223, I.227 Chain D: F.188, M.191, T.192, L.193, M.226 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.223, C:I.227, D:L.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, L. et al., Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel. Mol.Pharmacol. (2019)

Release Date

2019-10-23

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