MolNFT v1 · #164205 · protein

Crystal structure of viral rhodopsin olpvrii

6SQG: “Crystal structure of viral rhodopsin olpvrii”. X-ray diffraction, 3 ligands (LFA, RET, OLB), 14 pockets (best druggability 0.80). MolNFT v1 #164205 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SQG
Type: protein
Length: 1,051 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Viral rhodopsin olpvrii
UniProt: F2Y2Z0
Ligands: LFA, RET, OLB
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 84% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Viral rhodopsin olpvrii	protein	210	85% helix, 1% strand	F2Y2Z0
C	Viral rhodopsin olpvrii	protein	209	83% helix, 1% strand	F2Y2Z0
E	Viral rhodopsin olpvrii	protein	212	83% helix, 1% strand	F2Y2Z0

Ligands and binding sites

LFA · Eicosane · ligand · 71 copies · chains A, E, C, B, D
RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains D, E, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.80	0.98	24	RET
2	126	0.80	0.97	24	RET
3	124	0.80	0.97	25	RET
4	125	0.80	0.97	25	RET
5	122	0.80	0.97	22	RET

Interfaces

5 interfaces between chains.

A–E · 1366 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 1297 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1282 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1268 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1247 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 cofactor (retinal Schiff base).

Compared structures

6SQG · Crystal structure of viral rhodopsin OLPVRII · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt F2Y2Z0
Elsewhere: RCSB PDB 6SQG · PDBe 6SQG · UniProt F2Y2Z0

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