SMTL ID : 7v62.1

Crystal structure of human OSBP ORD in complex with cholesterol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-tetramer

Ligands

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 17 residues within 4Å: Chain A: M.20, M.33, F.37, M.43, R.46, D.50, S.80, Y.81, T.84, T.88, S.89, K.90, P.91, I.142, I.153, K.174, I.189 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.46, A:Y.81, A:K.90, A:P.91, A:I.142, A:I.153, A:I.189 Hydrogen bonds: A:S.80, A:K.174 CLR.6: 15 residues within 4Å: Chain B: M.20, M.43, R.46, D.50, S.80, Y.81, T.84, T.88, S.89, K.90, P.91, I.142, I.153, K.174, I.189 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.81, B:K.90, B:P.91, B:I.153, B:I.189 Hydrogen bonds: B:S.80, B:S.80 CLR.9: 14 residues within 4Å: Chain C: F.37, M.43, R.46, D.50, S.80, Y.81, T.84, S.89, K.90, P.91, I.142, L.151, K.174, I.189 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.37, C:R.46, C:Y.81, C:K.90, C:P.91, C:I.142, C:I.189 Hydrogen bonds: C:S.80 CLR.13: 15 residues within 4Å: Chain D: F.37, M.43, R.46, D.50, S.80, Y.81, S.89, K.90, P.91, I.142, L.151, I.153, K.174, V.179, I.189 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:R.46, D:Y.81, D:K.90, D:P.91, D:I.142, D:L.151, D:I.153, D:K.174, D:V.179, D:I.189 Hydrogen bonds: D:S.80, D:S.80

6 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 4 residues within 4Å: Chain A: C.391, K.394, D.396, S.398 No protein-ligand interaction detected (PLIP) DTT.3: 2 residues within 4Å: Chain A: C.23, K.30 No protein-ligand interaction detected (PLIP) DTT.7: 2 residues within 4Å: Chain B: N.22, C.23 No protein-ligand interaction detected (PLIP) DTT.10: 4 residues within 4Å: Chain C: K.62, C.63, E.68, Y.72 No protein-ligand interaction detected (PLIP) DTT.11: 2 residues within 4Å: Chain C: C.23, P.32 No protein-ligand interaction detected (PLIP) DTT.14: 4 residues within 4Å: Chain D: N.22, C.23, K.26, P.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.22

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 7 residues within 4Å: Chain A: L.96, H.119, H.120, R.344, R.347 Chain D: K.145, R.147 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain A Salt bridges: D:K.145, D:R.147, A:R.344, A:R.344, A:R.347, A:R.347 Hydrogen bonds: A:H.119, A:H.120

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 6 residues within 4Å: Chain A: L.28, S.29, M.43, K.90, P.91, N.93 No protein-ligand interaction detected (PLIP) DMS.8: 3 residues within 4Å: Chain B: S.118, R.347 Chain C: K.145 No protein-ligand interaction detected (PLIP) DMS.12: 5 residues within 4Å: Chain B: K.145 Chain C: S.118, H.119, H.120, R.347 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.145 DMS.15: 3 residues within 4Å: Chain D: L.96, H.119, R.347 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, J. et al., Ligand Recognition by the Lipid Transfer Domain of Human OSBP Is Important for Enterovirus Replication. Acs Infect Dis. (2022)

Release Date

2022-06-08

Peptides

Oxysterol-binding protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Oxysterol-binding protein 1