MolNFT v1 · #151559 · protein

Crystal structure of M. tuberculosis FADB2 (RV0468)

6HRD · 3-hydroxybutyryl-CoA dehydrogenase: “Crystal structure of M. tuberculosis FADB2 (RV0468)”. X-ray diffraction, 18 pockets (best druggability 0.84). MolNFT v1 #151559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6HRD
Type: protein
Length: 1,710 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-hydroxybutyryl-CoA dehydrogenase
EC: 1.1.1.157
UniProt: P9WNP7
Pockets: 18 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157)	protein	285	52% helix, 14% strand	P9WNP7

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains E, F

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

Pockets

18 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	1041	0.84	0.85	89	GOL
2	420	0.69	0.81	53	empty
3	472	0.69	0.79	41	empty
4	433	0.68	0.80	47	empty
5	419	0.68	0.80	42	empty

Interfaces

7 interfaces between chains.

E–F · 1595 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 1567 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 1557 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 541 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 528 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6HRD · Crystal structure of M. tuberculosis FadB2 (Rv0468) · the same entry in another collection · chain F against F, TM-score 1.00
P9WNP7 · AlphaFold monomer V2.0 prediction for 3-hydroxybutyryl-CoA dehydrogenase (P9WNP7) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P9WNP7
Elsewhere: RCSB PDB 6HRD · PDBe 6HRD · UniProt P9WNP7

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