MolNFT v1 · #124262 · protein

Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from burkholderia xenovorans LB400

5K9Z: “Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from burkholderia xenovorans LB400”. X-ray diffraction, 13 pockets (best druggability 0.86). MolNFT v1 #124262 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5K9Z
Type: protein
Length: 1,022 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative short-chain DEHYDROGENASE/REDUCTASE
UniProt: Q13HC1
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	244	50% helix, 18% strand	Q13HC1
B, C	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	266	51% helix, 17% strand	Q13HC1
D	Putative short-chain DEHYDROGENASE/REDUCTASE	protein	246	48% helix, 18% strand	Q13HC1

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains A, B, C, D

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

Pockets

13 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	911	0.86	0.88	59	empty
2	754	0.75	0.80	91	empty
3	609	0.74	0.81	75	empty
4	95	0.47	0.81	20	empty
5	97	0.44	0.79	16	empty

Interfaces

6 interfaces between chains.

B–C · 1763 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 1717 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1598 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1597 Å² buried · 24 hydrogen bonds · protein-protein
B–D · 1475 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5K9Z · Crystal Structure of 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 Q13HC1
Elsewhere: RCSB PDB 5K9Z · PDBe 5K9Z · UniProt Q13HC1

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