MolNFT v1 · #138488 · protein

3.2-ångström in situ mylar structure of bovine opsin at 100 K

5WKT · Rhodopsin: “3.2-ångström in situ mylar structure of bovine opsin at 100 K”. X-ray diffraction, 5 ligands (NAG, GLC, BMA), 4 pockets (best druggability 0.85). MolNFT v1 #138488 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5WKT
Type: protein
Length: 337 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin; Transducin galpha peptide
UniProt: P02699
Ligands: NAG, GLC, BMA, MAN, SO4
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	326	70% helix, 4% strand	P02699
B	Transducin galpha peptide	protein	11	55% helix, 0% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
SO4 · Sulfate ion · ion · chains B
BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	263	0.85	0.96	34	BOG
2	123	0.53	0.82	19	empty
3	78	0.47	0.82	25	empty
4	58	0.33	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 663 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 disulfide, 1 glycan (additive adduct, disulfide, N-glycosylation).

Compared structures

5WKT · 3.2-Angstrom In situ Mylar structure of bovine opsin at 100 K · the same entry in another collection · chain A against A, TM-score 1.00
P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A 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 P02699
Elsewhere: RCSB PDB 5WKT · PDBe 5WKT · UniProt P02699

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