MolNFT v1 · #82849 · protein

Crystal structure of phab from ralstonia eutropha

3VZP · Acetoacetyl-CoA reductase: “Crystal structure of phab from ralstonia eutropha”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.87). MolNFT v1 #82849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VZP
Type: protein
Length: 987 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetoacetyl-CoA reductase
EC: 1.1.1.36
UniProt: P14697
Ligands: SO4
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetoacetyl-CoA reductase (EC 1.1.1.36)	protein	245	51% helix, 16% strand	P14697
B, D	Acetoacetyl-CoA reductase (EC 1.1.1.36)	protein	249	50% helix, 15% strand	P14697
C	Acetoacetyl-CoA reductase (EC 1.1.1.36)	protein	244	52% helix, 16% strand	P14697

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, D
DIO · 1,4-diethylene dioxide · additive · 7 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, D, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	824	0.87	0.90	75	empty
2	907	0.78	0.80	85	SO4, DIO
3	409	0.72	0.83	53	SO4, DIO
4	402	0.70	0.82	52	SO4, DIO
5	389	0.69	0.81	50	SO4, DIO

Interfaces

6 interfaces between chains.

A–D · 1772 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1766 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1428 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1403 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 166 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3VZP · Crystal structure of PhaB from Ralstonia eutropha · the same entry in another collection · chain A against A, TM-score 1.00
P14697 · AlphaFold monomer V2.0 prediction for acetoacetyl-CoA reductase (P14697) · a predicted model of the same protein · 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 P14697
Elsewhere: RCSB PDB 3VZP · PDBe 3VZP · UniProt P14697

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