Research workbench

Deinococcus radiodurans bphp photosensory module

Analyse Deinococcus radiodurans bphp photosensory module in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q0J
Type: protein
Length: 495 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
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriophytochrome (EC 2.7.13.3)	protein	495	34% helix, 25% 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

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

Pockets

5 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	401	0.82	0.90	57	LBV
2	161	0.55	0.80	31	empty
3	73	0.46	0.82	20	empty
4	76	0.33	0.75	19	empty
5	91	0.30	0.71	14	empty

Modifications

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

Compared structures

4Q0J · Deinococcus radiodurans BphP photosensory module · 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 0.99

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 Q9RZA4
Elsewhere: RCSB PDB 4Q0J · PDBe 4Q0J · UniProt Q9RZA4

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