SMTL ID : 6sqg.1

Crystal structure of viral rhodopsin OLPVRII

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-4-1-mer

Ligands

71 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.1: 4 residues within 4Å: Chain A: S.104, M.107, G.111 Ligands: LFA.2 Ligand excluded by PLIP LFA.2: 6 residues within 4Å: Chain A: G.111, M.112, Y.114, G.115 Ligands: LFA.1, LFA.9 Ligand excluded by PLIP LFA.3: 6 residues within 4Å: Chain A: G.20, T.21, F.24, V.47, A.50 Ligands: LFA.51 Ligand excluded by PLIP LFA.4: 8 residues within 4Å: Chain A: T.21 Chain C: M.17, G.20, T.21, F.24, T.43, V.47, A.50 Ligand excluded by PLIP LFA.5: 1 residues within 4Å: Chain A: G.163 Ligand excluded by PLIP LFA.6: 4 residues within 4Å: Chain A: F.175, V.189, L.190, F.193 Ligand excluded by PLIP LFA.7: 4 residues within 4Å: Chain A: F.175, P.182, V.185, G.186 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: I.82 Chain E: F.15, I.200 Ligands: OLB.63 Ligand excluded by PLIP LFA.9: 4 residues within 4Å: Chain A: M.112, Y.146 Ligands: LFA.2, LFA.12 Ligand excluded by PLIP LFA.10: 5 residues within 4Å: Chain A: F.197, Y.201, F.210 Chain C: F.103 Ligands: LFA.36 Ligand excluded by PLIP LFA.11: 8 residues within 4Å: Chain A: V.135, F.138, L.139, G.142, N.149, R.152, Y.162 Ligands: LFA.17 Ligand excluded by PLIP LFA.12: 5 residues within 4Å: Chain A: L.139, F.140, G.143 Ligands: LFA.9, LFA.16 Ligand excluded by PLIP LFA.13: 8 residues within 4Å: Chain A: Y.73, V.74, Y.121 Chain E: Y.7, S.8, L.11 Ligands: LFA.14, LFA.71 Ligand excluded by PLIP LFA.14: 5 residues within 4Å: Chain A: A.77, Y.114 Chain E: F.197 Ligands: LFA.13, LFA.71 Ligand excluded by PLIP LFA.15: 3 residues within 4Å: Chain A: A.164, F.193, Y.201 Ligand excluded by PLIP LFA.16: 2 residues within 4Å: Chain A: Y.146 Ligands: LFA.12 Ligand excluded by PLIP LFA.17: 3 residues within 4Å: Chain A: F.138, V.174 Ligands: LFA.11 Ligand excluded by PLIP LFA.19: 4 residues within 4Å: Chain A: L.28 Chain C: L.28 Chain D: F.24 Chain E: L.28 Ligand excluded by PLIP LFA.20: 6 residues within 4Å: Chain B: M.17, G.20, T.21, F.24, T.43 Ligands: LFA.54 Ligand excluded by PLIP LFA.21: 7 residues within 4Å: Chain B: L.160, L.161, G.163, A.164, F.193, V.198 Ligands: LFA.29 Ligand excluded by PLIP LFA.22: 6 residues within 4Å: Chain B: F.197, I.200, Y.201, F.210 Chain D: I.82, F.103 Ligand excluded by PLIP LFA.23: 5 residues within 4Å: Chain B: L.41, I.82 Chain C: I.22, I.200 Ligands: LFA.42 Ligand excluded by PLIP LFA.24: 6 residues within 4Å: Chain B: Y.73, Y.114 Chain C: L.4, Y.7, S.8, L.11 Ligand excluded by PLIP LFA.25: 6 residues within 4Å: Chain B: G.142, F.145, Y.146, N.149, Y.162, F.166 Ligand excluded by PLIP LFA.26: 5 residues within 4Å: Chain B: M.112, L.136, L.139, F.140 Ligands: LFA.27 Ligand excluded by PLIP LFA.27: 4 residues within 4Å: Chain B: I.108, M.112, K.147 Ligands: LFA.26 Ligand excluded by PLIP LFA.28: 5 residues within 4Å: Chain B: L.4, Y.7, S.8, V.185 Ligands: LFA.59 Ligand excluded by PLIP LFA.29: 5 residues within 4Å: Chain B: L.4, F.175, L.181, P.182 Ligands: LFA.21 Ligand excluded by PLIP LFA.30: 3 residues within 4Å: Chain B: G.111, M.112 Ligands: LFA.33 Ligand excluded by PLIP LFA.31: 2 residues within 4Å: Chain B: G.118, T.119 Ligand excluded by PLIP LFA.32: 4 residues within 4Å: Chain B: M.107, G.111, Y.114 Ligands: LFA.33 Ligand excluded by PLIP LFA.33: 3 residues within 4Å: Chain B: I.108 Ligands: LFA.30, LFA.32 Ligand excluded by PLIP LFA.35: 4 residues within 4Å: Chain C: G.163, A.164, F.193, Y.201 Ligand excluded by PLIP LFA.36: 4 residues within 4Å: Chain A: F.15, F.197 Chain C: I.82 Ligands: LFA.10 Ligand excluded by PLIP LFA.37: 5 residues within 4Å: Chain C: V.135, F.138, L.139, G.142 Ligands: LFA.40 Ligand excluded by PLIP LFA.38: 4 residues within 4Å: Chain C: M.107, I.108, G.111 Ligands: LFA.48 Ligand excluded by PLIP LFA.39: 5 residues within 4Å: Chain C: I.108, G.111, M.112, G.115, F.140 Ligand excluded by PLIP LFA.40: 4 residues within 4Å: Chain C: G.142, Y.146, Y.162 Ligands: LFA.37 Ligand excluded by PLIP LFA.41: 3 residues within 4Å: Chain A: S.8, L.11 Chain C: L.117 Ligand excluded by PLIP LFA.42: 3 residues within 4Å: Chain B: F.103 Chain C: Y.201 Ligands: LFA.23 Ligand excluded by PLIP LFA.43: 6 residues within 4Å: Chain C: F.175, L.181, P.182, V.185, G.186 Ligands: LFA.45 Ligand excluded by PLIP LFA.44: 3 residues within 4Å: Chain C: M.112, L.139, F.140 Ligand excluded by PLIP LFA.45: 2 residues within 4Å: Chain C: L.190 Ligands: LFA.43 Ligand excluded by PLIP LFA.46: 4 residues within 4Å: Chain C: D.159, Y.162, G.163, F.166 Ligand excluded by PLIP LFA.47: 2 residues within 4Å: Chain C: F.103, S.104 Ligand excluded by PLIP LFA.48: 1 residues within 4Å: Ligands: LFA.38 Ligand excluded by PLIP LFA.51: 8 residues within 4Å: Chain D: T.21 Chain E: G.20, T.21, F.24, T.43, V.47, A.50 Ligands: LFA.3 Ligand excluded by PLIP LFA.52: 4 residues within 4Å: Chain D: G.163, A.164, F.193 Ligands: LFA.60 Ligand excluded by PLIP LFA.53: 4 residues within 4Å: Chain D: F.175, L.181, P.182, V.189 Ligand excluded by PLIP LFA.54: 8 residues within 4Å: Chain B: T.21 Chain D: M.17, G.20, T.21, F.24, V.47, A.50 Ligands: LFA.20 Ligand excluded by PLIP LFA.55: 6 residues within 4Å: Chain D: G.163, F.166, V.167 Ligands: LFA.56, LFA.58, LFA.61 Ligand excluded by PLIP LFA.56: 7 residues within 4Å: Chain D: G.142, N.149, R.152, D.159, Y.162 Ligands: LFA.55, LFA.57 Ligand excluded by PLIP LFA.57: 4 residues within 4Å: Chain D: T.134, F.138 Ligands: LFA.56, LFA.58 Ligand excluded by PLIP LFA.58: 6 residues within 4Å: Chain D: F.138, V.174, Q.177 Ligands: LFA.55, LFA.57, LFA.61 Ligand excluded by PLIP LFA.59: 10 residues within 4Å: Chain B: Y.7, L.11, F.15, F.197 Chain D: Y.73, Y.114, L.117, G.118, Y.121 Ligands: LFA.28 Ligand excluded by PLIP LFA.60: 3 residues within 4Å: Chain D: L.171, L.190 Ligands: LFA.52 Ligand excluded by PLIP LFA.61: 3 residues within 4Å: Chain D: A.170 Ligands: LFA.55, LFA.58 Ligand excluded by PLIP LFA.64: 4 residues within 4Å: Chain E: V.135, F.138, L.139 Ligands: LFA.65 Ligand excluded by PLIP LFA.65: 6 residues within 4Å: Chain E: F.138, F.141, G.142, V.174 Ligands: LFA.64, LFA.67 Ligand excluded by PLIP LFA.66: 2 residues within 4Å: Chain E: M.107, Y.114 Ligand excluded by PLIP LFA.67: 6 residues within 4Å: Chain E: G.142, Y.146, N.149, Y.162, F.166 Ligands: LFA.65 Ligand excluded by PLIP LFA.68: 3 residues within 4Å: Chain D: I.200 Chain E: I.82 Ligands: OLB.50 Ligand excluded by PLIP LFA.69: 4 residues within 4Å: Chain E: M.112, L.139, F.140, G.143 Ligand excluded by PLIP LFA.70: 3 residues within 4Å: Chain D: L.11 Chain E: Y.73, Y.121 Ligand excluded by PLIP LFA.71: 4 residues within 4Å: Chain E: V.189, F.193 Ligands: LFA.13, LFA.14 Ligand excluded by PLIP LFA.72: 7 residues within 4Å: Chain E: D.159, G.163, A.164, L.168, V.198, Y.201 Ligands: LFA.73 Ligand excluded by PLIP LFA.73: 8 residues within 4Å: Chain E: L.171, F.175, L.181, P.182, V.185, V.189, L.190 Ligands: LFA.72 Ligand excluded by PLIP LFA.74: 3 residues within 4Å: Chain E: I.128 Ligands: LFA.75, LFA.76 Ligand excluded by PLIP LFA.75: 2 residues within 4Å: Chain E: M.132 Ligands: LFA.74 Ligand excluded by PLIP LFA.76: 2 residues within 4Å: Ligands: LFA.74, LFA.77 Ligand excluded by PLIP LFA.77: 5 residues within 4Å: Chain E: G.118, L.122, I.125, V.127 Ligands: LFA.76 Ligand excluded by PLIP

5 x RET: RETINAL(Covalent)

RET.18: 18 residues within 4Å: Chain A: W.76, T.79, T.80, M.83, M.116, L.117, G.120, G.133, G.137, F.138, W.169, Y.172, G.173, Y.176, Y.187, D.191, S.194, K.195 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.76, A:W.76, A:T.80, A:L.117, A:F.138, A:W.169, A:W.169, A:Y.172, A:Y.172, A:Y.172, A:Y.172, A:K.195 RET.34: 18 residues within 4Å: Chain B: W.76, T.79, T.80, M.83, M.116, G.120, G.133, G.137, F.138, F.141, W.169, Y.172, G.173, Y.176, Y.187, D.191, S.194, K.195 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.76, B:T.80, B:F.141, B:W.169, B:W.169, B:Y.172, B:Y.172, B:Y.172, B:Y.172, B:Y.172, B:K.195 RET.49: 16 residues within 4Å: Chain C: W.76, T.79, T.80, M.83, M.116, G.120, G.133, G.137, F.138, W.169, Y.172, G.173, Y.176, D.191, S.194, K.195 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.76, C:W.76, C:T.80, C:F.138, C:W.169, C:W.169, C:Y.172, C:Y.172, C:Y.172, C:Y.172, C:Y.172, C:K.195 RET.62: 16 residues within 4Å: Chain D: W.76, T.79, T.80, M.83, M.116, L.117, G.120, G.137, F.138, W.169, Y.172, G.173, Y.176, D.191, S.194, K.195 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.76, D:W.76, D:T.80, D:W.169, D:W.169, D:Y.172, D:Y.172, D:Y.172, D:Y.172, D:Y.176, D:K.195 RET.78: 18 residues within 4Å: Chain E: W.76, T.79, T.80, M.83, M.116, L.117, G.120, G.133, G.137, F.138, W.169, Y.172, G.173, Y.176, Y.187, D.191, S.194, K.195 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:W.76, E:W.76, E:T.80, E:L.117, E:F.138, E:W.169, E:W.169, E:Y.172, E:Y.172, E:Y.172, E:Y.172, E:Y.172, E:K.195

2 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.50: 6 residues within 4Å: Chain D: Y.201, F.205, K.208, F.210 Chain E: F.103 Ligands: LFA.68 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.201, D:F.210, D:F.210, E:F.103 OLB.63: 7 residues within 4Å: Chain A: F.103 Chain E: F.197, Y.201, F.205, K.208, F.210 Ligands: LFA.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain E Hydrophobic interactions: A:F.103, E:F.197, E:F.210 Hydrogen bonds: E:F.205 Water bridges: E:F.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bratanov, D. et al., Unique structure and function of viral rhodopsins. Nat Commun (2019)

Release Date

2019-11-06

Peptides

viral rhodopsin OLPVRII: ABCD
viral rhodopsin OLPVRII: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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viral rhodopsin OLPVRII

viral rhodopsin OLPVRII