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Crystal structure of all-trans green fluorescent protein

Analyse Crystal structure of all-trans green fluorescent protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LW5
Type: protein
Length: 1,125 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent protein
UniProt: P42212
Ligands: CRO
Pockets: 17 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Green fluorescent protein	protein	225	9% helix, 51% strand	P42212
B	Green fluorescent protein	protein	226	8% helix, 52% strand	P42212
C	Green fluorescent protein	protein	225	11% helix, 52% strand	P42212
D	Green fluorescent protein	protein	224	11% 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 · 5 copies · chains A, B, C, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	901	0.79	0.81	73	empty
2	106	0.78	0.98	26	CRO
3	100	0.78	0.98	27	CRO
4	95	0.77	0.97	26	CRO
5	95	0.77	0.97	32	CRO

Interfaces

4 interfaces between chains.

A–B · 689 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 469 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 325 Å² buried · 5 hydrogen bonds · protein-protein
C–E · 119 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 cofactor (chromophore).

Compared structures

4LW5 · Crystal structure of all-trans green fluorescent protein · the same entry in another collection · chain E against E, 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 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 4LW5 · PDBe 4LW5 · UniProt P42212

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