Research workbench

Green fluorescent protein mutant F99S, M153T and V163A

Analyse Green fluorescent protein mutant F99S, M153T and V163A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B9C
Type: protein
Length: 896 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (green fluorescent protein)
UniProt: P42212
Ligands: CRO
Pockets: 15 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein (green fluorescent protein)	protein	224	8% helix, 53% 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

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

Pockets

15 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	461	0.74	0.84	68	empty
2	56	0.73	0.99	23	CRO
3	56	0.72	0.99	22	CRO
4	52	0.72	0.99	20	CRO
5	57	0.71	0.98	22	CRO

Interfaces

5 interfaces between chains.

A–B · 1008 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 967 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 727 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 157 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (chromophore).

Compared structures

1B9C · Green Fluorescent Protein Mutant F99S, M153T and V163A · 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 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 1B9C · PDBe 1B9C · UniProt P42212

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