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Crystal structure of jumping spider rhodopsin-1 bound to 9-cis retinal

Analyse Crystal structure of jumping spider rhodopsin-1 bound to 9-cis retinal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I9K
Type: protein
Length: 310 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KUMOPSIN1
UniProt: B1B1U5
Ligands: RET
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 78% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KUMOPSIN1	protein	310	78% helix, 2% strand	B1B1U5

Ligands and binding sites

RET · Retinal · ligand · chains A
OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 11 copies · chains A

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

Pockets

2 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	171	0.84	0.98	29	RET
2	227	0.53	0.77	31	empty

Modifications

Observed in the structure: 1 cofactor, 1 disulfide (retinal Schiff base, disulfide).

Compared structures

6I9K · Crystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal · 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 B1B1U5
Elsewhere: RCSB PDB 6I9K · PDBe 6I9K · UniProt B1B1U5

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