Research workbench

Photoconverted hcred in its optoacoustic state

Analyse Photoconverted hcred in its optoacoustic state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y1G
Type: protein
Length: 884 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GFP-like non-fluorescent chromoprotein
UniProt: Q95W85
Ligands: CRU
Pockets: 10 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	GFP-like non-fluorescent chromoprotein	protein	221	5% helix, 56% strand	Q95W85

Ligands and binding sites

CRU · 4-[(4Z)-1-(carboxymethyl)-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-2-yl]-4-iminobutanoic acid · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 19 copies · chains A, D, B, C

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	939	0.86	0.88	99	EDO
2	98	0.78	0.98	29	CRU
3	100	0.76	0.97	28	CRU
4	59	0.70	0.97	20	CRU
5	63	0.70	0.97	19	CRU

Interfaces

6 interfaces between chains.

A–B · 1665 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1619 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 853 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 851 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 101 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

6Y1G · Photoconverted HcRed in its optoacoustic state · the same entry in another collection · chain A against A, TM-score 1.00
Q95W85 · AlphaFold monomer V2.0 prediction for GFP-like non-fluorescent chromoprotein (Q95W85) · a predicted model of the same protein · 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 Q95W85
Elsewhere: RCSB PDB 6Y1G · PDBe 6Y1G · UniProt Q95W85

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