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Crystal structure of the lumi intermediate of squid rhodopsin

Analyse Crystal structure of the lumi intermediate of squid rhodopsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WW3
Type: protein
Length: 697 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P31356
Ligands: PLM, RET, TWT, PC1, SO4
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	350	73% helix, 2% strand	P31356
B	Rhodopsin	protein	347	72% helix, 2% strand	P31356

Ligands and binding sites

PLM · Palmitic acid · ligand · 4 copies · chains A, B
RET · Retinal · ligand · 2 copies · chains A, B
TWT · Docosane · ligand · 2 copies · chains A, B
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · chains B
SO4 · Sulfate ion · ion · chains B
BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.82	0.97	28	RET
2	141	0.81	0.97	29	RET
3	348	0.69	0.82	51	BOG
4	288	0.68	0.83	40	BOG
5	57	0.40	0.80	14	empty

Interfaces

1 interface between chains.

A–B · 489 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor, 2 disulfide (retinal Schiff base, disulfide).

Compared structures

4WW3 · Crystal structure of the lumi intermediate of squid rhodopsin · the same entry in another collection · chain A against A, TM-score 1.00
P31356 · AlphaFold monomer V2.0 prediction for rhodopsin (P31356) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P31356
Elsewhere: RCSB PDB 4WW3 · PDBe 4WW3 · UniProt P31356

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