MolNFT v1 · #106842 · protein

Crystal structure of a putative putative D-beta-hydroxybutyrate dehydrogenase from burkholderia cenocepacia J2315

4TRR: “Crystal structure of a putative putative D-beta-hydroxybutyrate dehydrogenase from burkholderia cenocepacia…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.82). MolNFT v1 #106842 on GenesisL1: 3D structure…

PDB: 4TRR
Type: protein
Length: 2,006 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative D-beta-hydroxybutyrate dehydrogenase
UniProt: B4EG08
Ligands: SO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Putative D-beta-hydroxybutyrate dehydrogenase	protein	256	52% helix, 17% strand	B4EG08
B	Putative D-beta-hydroxybutyrate dehydrogenase	protein	260	52% helix, 15% strand	B4EG08
D	Putative D-beta-hydroxybutyrate dehydrogenase	protein	256	51% helix, 16% strand	B4EG08
E	Putative D-beta-hydroxybutyrate dehydrogenase	protein	242	50% helix, 17% strand	B4EG08
F	Putative D-beta-hydroxybutyrate dehydrogenase	protein	254	49% helix, 17% strand	B4EG08
G	Putative D-beta-hydroxybutyrate dehydrogenase	protein	226	46% helix, 17% strand	B4EG08
H	Putative D-beta-hydroxybutyrate dehydrogenase	protein	256	50% helix, 17% strand	B4EG08

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, H
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D, F, G

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	233	0.82	0.95	32	empty
2	248	0.82	0.94	32	empty
3	1098	0.78	0.80	122	SO4
4	1124	0.77	0.79	117	SO4
5	731	0.74	0.79	82	empty

Interfaces

13 interfaces between chains.

E–H · 1650 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1648 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1636 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1607 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1281 Å² buried · 20 hydrogen bonds · protein-protein

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 B4EG08
Elsewhere: RCSB PDB 4TRR · PDBe 4TRR · UniProt B4EG08

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