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Crystal structure of a photoactivated rhodopsin

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

PDB: 2I37
Type: protein
Length: 954 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin
UniProt: P02699
Ligands: ACE, NAG, MAN, BMA
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 61% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodopsin	protein	317	61% helix, 4% strand	P02699
B	Rhodopsin	protein	319	62% helix, 4% strand	P02699
C	Rhodopsin	protein	318	60% helix, 4% strand	P02699

Ligands and binding sites

ACE · Acetyl group · ligand · 3 copies · chains A, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
BMA · beta-D-mannopyranose · sugar

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	761	0.84	0.86	68	empty
2	180	0.77	0.93	27	empty
3	180	0.77	0.93	31	empty
4	875	0.69	0.74	51	empty
5	52	0.67	0.96	22	empty

Interfaces

2 interfaces between chains.

B–C · 679 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 422 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 3 covalent, 3 disulfide (N-glycosylation, covalent ligand, disulfide).

Compared structures

2I37 · Crystal structure of a photoactivated rhodopsin · the same entry in another collection · chain C against C, 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 0.93

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 2I37 · PDBe 2I37 · UniProt P02699

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