SMTL ID : 5zm6.1

Crystal structure of ORP1-ORD in complex with PI(4,5)P2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x IEP: [(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate(Non-covalent)

IEP.1: 15 residues within 4Å: Chain A: M.44, R.57, T.99, G.100, K.101, P.102, N.104, H.129, H.130, V.190, K.371, E.375, R.379, R.382 Chain B: G.159 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.101 Hydrogen bonds: A:N.104, A:N.104, A:E.375, A:E.375, A:R.382 Salt bridges: A:K.101, A:H.129, A:H.130, A:H.130, A:K.371, A:R.379 IEP.3: 18 residues within 4Å: Chain A: W.158 Chain B: M.44, F.54, R.57, T.99, K.101, P.102, N.104, H.129, H.130, P.131, P.132, L.155, V.162, V.190, I.193, E.375, R.379 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.54, B:K.101, B:K.101, B:H.130, B:P.132, B:V.162, B:V.190, A:W.158 Hydrogen bonds: B:N.104, B:E.375 Salt bridges: B:K.101, B:K.101, B:H.129, B:H.130, B:H.130, B:R.379 IEP.5: 15 residues within 4Å: Chain C: M.44, R.57, T.99, G.100, K.101, P.102, N.104, H.129, H.130, V.190, K.371, E.375, R.379, R.382 Chain D: G.159 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.101 Hydrogen bonds: C:N.104, C:N.104, C:E.375, C:E.375, C:E.375, C:R.382 Salt bridges: C:K.101, C:H.129, C:H.130, C:H.130, C:K.371, C:R.379 IEP.7: 18 residues within 4Å: Chain C: W.158 Chain D: M.44, F.54, R.57, T.99, K.101, P.102, N.104, H.129, H.130, P.131, P.132, L.155, V.162, V.190, I.193, E.375, R.379 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.54, D:K.101, D:K.101, D:H.130, D:P.132, D:V.162, D:V.190, C:W.158 Hydrogen bonds: D:N.104, D:E.375 Salt bridges: D:K.101, D:K.101, D:H.129, D:H.130, D:H.130, D:R.379

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: R.121, Y.412, S.415, Y.416, W.417, D.418 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.415, A:W.417 Salt bridges: A:R.121 ACT.4: 5 residues within 4Å: Chain B: Y.412, G.414, S.415, Y.416, D.418 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.412, B:Y.412, B:S.415, B:Y.416 ACT.6: 6 residues within 4Å: Chain C: R.121, Y.412, S.415, Y.416, W.417, D.418 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.412, C:S.415, C:W.417 Salt bridges: C:R.121 ACT.8: 5 residues within 4Å: Chain D: Y.412, G.414, S.415, Y.416, D.418 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.412, D:S.415, D:Y.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P2/PI(3,4)P2. Nat Commun (2019)

Release Date

2019-02-27

Peptides

Oxysterol-binding protein-related protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Oxysterol-binding protein-related protein 1

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