Research workbench

X-ray structure of REQY1 (oxidized form)

Analyse X-ray structure of REQY1 (oxidized form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AA2
Type: protein
Length: 689 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CR2
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	223	11% helix, 53% strand	P42212
B, C	Green fluorescent protein	protein	233	13% helix, 51% strand	P42212

Ligands and binding sites

CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 3 copies · chains A, B, C

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

Pockets

9 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	50	0.70	0.99	16	CR2
2	50	0.70	0.98	19	CR2
3	67	0.36	0.77	14	empty
4	63	0.36	0.78	18	empty
5	70	0.35	0.76	16	empty

Interfaces

3 interfaces between chains.

A–C · 378 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 50 Å² buried · 1 hydrogen bond · protein-protein
A–B · 43 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor, 3 disulfide (chromophore, disulfide).

Compared structures

6AA2 · X-ray structure of ReQy1 (oxidized form) · the same entry in another collection · chain A against A, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · 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 P42212
Elsewhere: RCSB PDB 6AA2 · PDBe 6AA2 · UniProt P42212

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