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Crystal structure of an oxidoreductase from burkholderia vietnamiensis

Analyse Crystal structure of an oxidoreductase from burkholderia vietnamiensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IDX
Type: protein
Length: 524 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain DEHYDROGENASE/REDUCTASE sdr
UniProt: A4JGH3
Ligands: SO4
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	261	51% helix, 15% strand	A4JGH3
B	Short-chain DEHYDROGENASE/REDUCTASE sdr	protein	263	50% helix, 15% strand	A4JGH3

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B

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

Pockets

3 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	622	0.71	0.79	59	SO4
2	648	0.70	0.78	59	SO4
3	468	0.63	0.77	33	empty

Interfaces

1 interface between chains.

A–B · 1383 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5IDX · Crystal structure of an oxidoreductase from Burkholderia vietnamiensis · 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 A4JGH3
Elsewhere: RCSB PDB 5IDX · PDBe 5IDX · UniProt A4JGH3

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