SMTL ID : 6juh.1

structure of CavAb in complex with efonidipine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

MC3.1: 9 residues within 4Å: Chain A: T.138, F.141, T.162, G.164, E.165, F.167, Y.168 Chain B: W.195, F.203 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.141, B:F.203 Hydrogen bonds: A:T.162 MC3.5: 7 residues within 4Å: Chain B: F.141, T.162, G.164, F.167, Y.168 Chain C: W.195 Ligands: G3P.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.141 Hydrogen bonds: B:E.165, C:W.195 MC3.8: 9 residues within 4Å: Chain C: F.141, T.162, G.164, E.165, F.167, Y.168, F.171 Chain D: W.195 Ligands: G3P.11 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:W.195 Hydrophobic interactions: C:F.141, C:F.171 MC3.14: 9 residues within 4Å: Chain A: Y.193, W.195, F.203 Chain D: F.141, G.164, E.165, F.167, Y.168, F.171 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.141, D:F.171, D:F.171, A:F.203

4 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.2: 5 residues within 4Å: Chain A: F.152, Y.191, Y.193, A.194 Chain D: I.97 No protein-ligand interaction detected (PLIP) PX4.6: 1 residues within 4Å: Chain B: Y.191 No protein-ligand interaction detected (PLIP) PX4.9: 2 residues within 4Å: Chain C: I.97 Chain D: Y.191 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.191 PX4.10: 2 residues within 4Å: Chain C: L.151, Y.191 No protein-ligand interaction detected (PLIP)

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

G3P.3: 3 residues within 4Å: Chain A: S.34 Chain B: T.162 Ligands: MC3.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.36 G3P.11: 4 residues within 4Å: Chain C: T.162, L.163, G.164 Ligands: MC3.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.163, C:G.164 G3P.12: 2 residues within 4Å: Chain C: S.34, T.36 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.34, C:T.36 G3P.15: 7 residues within 4Å: Chain A: T.162, L.163, G.164 Chain D: G.30, S.34, K.35, T.36 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:L.163, A:G.164, D:K.35, D:T.36

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain B: D.178 Ligands: CA.7 No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain A: D.178 Chain B: D.178 Chain C: D.178 Chain D: D.178 Ligands: CA.4 No protein-ligand interaction detected (PLIP)

1 x C9X: 2-[phenyl-(phenylmethyl)amino]ethyl (4~{R})-5-(5,5-dimethyl-2-oxidanylidene-1,3,2$l^{5}-dioxaphosphinan-2-yl)-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3-carboxylate(Non-covalent)

C9X.13: 10 residues within 4Å: Chain A: M.174, T.175, L.176, T.206 Chain B: L.176, T.206, I.210 Chain D: T.175, L.176, I.210 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: A:L.176, A:L.176, A:T.206, B:L.176, B:I.210, D:I.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, F. et al., Structural basis for efonidipine block of a voltage-gated Ca2+channel. Biochem.Biophys.Res.Commun. (2019)

Release Date

2019-11-06

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