Research workbench

GFP/S205V mutant

Analyse GFP/S205V mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QLE
Type: protein
Length: 901 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Green fluorescent protein	protein	226	11% helix, 52% strand	P42212
B, C, D	Green fluorescent protein	protein	225	9% helix, 52% strand	P42212

Ligands and binding sites

CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
IMD · Imidazole · additive · 4 copies · chains A, B, D, C

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

Pockets

11 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	1104	0.82	0.83	126	empty
2	100	0.78	0.98	25	CRO
3	92	0.77	0.98	25	CRO
4	99	0.77	0.98	23	CRO
5	100	0.77	0.97	26	CRO

Interfaces

6 interfaces between chains.

A–B · 698 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 519 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 424 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 186 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 174 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

2QLE · GFP/S205V mutant · the same entry in another collection · chain D against D, TM-score 1.00
P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain D 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 P42212
Elsewhere: RCSB PDB 2QLE · PDBe 2QLE · UniProt P42212

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