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X-ray structure of benzoate dioxygenase reductase

Analyse X-ray structure of benzoate dioxygenase reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KRH
Type: protein
Length: 674 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Benzoate 1,2-dioxygenase reductase
EC: 1.18.1.3
UniProt: P07771
Ligands: FES, FAD, SO4
Pockets: 12 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Benzoate 1,2-dioxygenase reductase (EC 1.18.1.3)	protein	337	24% helix, 33% strand	P07771

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B
FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 5 copies · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.66	0.80	47	SO4, FAD
2	230	0.63	0.82	27	FAD
3	462	0.61	0.76	48	SO4
4	328	0.56	0.76	34	empty
5	97	0.56	0.85	22	empty

Interfaces

1 interface between chains.

A–B · 285 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1KRH · X-ray Structure of Benzoate Dioxygenase Reductase · the same entry in another collection · chain A against A, TM-score 1.00
P07771 · AlphaFold monomer V2.0 prediction for benzoate 1,2-dioxygenase electron transfer… · a predicted model of the same protein · chain B 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 P07771
Elsewhere: RCSB PDB 1KRH · PDBe 1KRH · UniProt P07771

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