MolNFT v1 · #93820 · protein

Crystal structure of the yellow fluorescent protein phiyfp (phialidium sp.)

4HE4: “Crystal structure of the yellow fluorescent protein phiyfp (phialidium sp.)”. X-ray diffraction, 1 ligand (CRO), 7 pockets (best druggability 0.78). MolNFT v1 #93820 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HE4
Type: protein
Length: 462 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yellow fluorescent protein
UniProt: Q6RYS7
Ligands: CRO
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Yellow fluorescent protein	protein	231	10% helix, 51% strand	Q6RYS7

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 · 2 copies · chains A, B

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

Pockets

7 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	117	0.78	0.97	31	CRO
2	89	0.76	0.97	21	CRO
3	97	0.39	0.76	20	empty
4	102	0.37	0.75	18	empty
5	76	0.32	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 1368 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (chromophore).

Compared structures

4HE4 · Crystal structure of the yellow fluorescent protein phiYFP (Phialidium sp.) · the same entry in another collection · 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 Q6RYS7
Elsewhere: RCSB PDB 4HE4 · PDBe 4HE4 · UniProt Q6RYS7

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