MolNFT v1 · #104097 · protein

Deinococcus radiodurans bphp pas-gaf

4Q0H · Bacteriophytochrome: “Deinococcus radiodurans bphp pas-gaf”. X-ray diffraction, 2 ligands (LBV, CL), 4 pockets (best druggability 0.80). MolNFT v1 #104097 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q0H
Type: protein
Length: 321 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriophytochrome
EC: 2.7.13.3
UniProt: Q9RZA4
Ligands: LBV, CL
Pockets: 4 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriophytochrome (EC 2.7.13.3)	protein	321	30% helix, 27% strand	Q9RZA4

Ligands and binding sites

LBV · 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid · ligand · chains A
CL · Chloride ion · ion · chains A
IPA · Isopropyl alcohol · additive · 3 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.80	0.91	35	LBV
2	150	0.55	0.81	31	empty
3	64	0.52	0.87	19	empty
4	95	0.48	0.80	16	empty

Modifications

Observed in the structure: 1 cofactor (biliverdin attachment).

Compared structures

4Q0H · Deinococcus radiodurans BphP PAS-GAF · the same entry in another collection · chain A against A, TM-score 1.00
Q9RZA4 · AlphaFold monomer V2.0 prediction for bacteriophytochrome (Q9RZA4) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9RZA4
Elsewhere: RCSB PDB 4Q0H · PDBe 4Q0H · UniProt Q9RZA4

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