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Crystal structure of a putative short-chain DEHYDROGENASE/REDUCTASE from burkholderia xenovorans

Analyse Crystal structure of a putative short-chain DEHYDROGENASE/REDUCTASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5JC8
Type: protein
Length: 1,030 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative short-chain DEHYDROGENASE/REDUCTASE
UniProt: Q13GE3
Ligands: MG
Pockets: 10 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	263	49% helix, 17% strand	Q13GE3
B	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	253	49% helix, 17% strand	Q13GE3
C	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	252	46% helix, 17% strand	Q13GE3
D	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	262	50% helix, 17% strand	Q13GE3

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
EDO · 1,2-ethanediol · additive · 13 copies · chains A, C, B, D
BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	991	0.85	0.86	61	empty
2	459	0.74	0.83	53	EDO, MG
3	435	0.72	0.83	40	empty
4	456	0.71	0.81	54	MG
5	435	0.69	0.80	47	empty

Interfaces

6 interfaces between chains.

B–D · 1642 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1631 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1531 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1527 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 540 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5JC8 · Crystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia… · 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 Q13GE3
Elsewhere: RCSB PDB 5JC8 · PDBe 5JC8 · UniProt Q13GE3

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