Research workbench

Rubredoxin OXYGEN:OXIDOREDUCTASE (roo) from anaerobe desulfovibrio gigas

Analyse Rubredoxin OXYGEN:OXIDOREDUCTASE (roo) from anaerobe desulfovibrio gigas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E5D
Type: protein
Length: 802 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RUBREDOXIN\:OXYGEN oxidoreductase
Ligands: FMN, FEO, OXY
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RUBREDOXIN\:OXYGEN oxidoreductase	protein	401	40% helix, 25% strand	—

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
FEO · Mu-oxo-diiron · ligand · 2 copies · chains A, B
OXY · Oxygen molecule · ion · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	167	0.81	0.96	30	FMN
2	163	0.79	0.95	30	FMN
3	75	0.65	0.91	23	empty
4	82	0.63	0.90	28	empty
5	115	0.49	0.80	20	empty

Interfaces

1 interface between chains.

A–B · 1912 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1E5D · Rubredoxin OXYGEN:OXIDOREDUCTASE (roo) from anaerobe desulfovibrio gigas · 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
Elsewhere: RCSB PDB 1E5D · PDBe 1E5D

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