MolNFT v1 · #111668 · protein

Pksg, a hmg-CoA synthase from bacillus subtilis

4YXQ · Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp…: “Pksg, a hmg-CoA synthase from bacillus subtilis”. X-ray diffraction, 15 pockets (best druggability 0.79). MolNFT v1 #111668 on GenesisL1: 3D structure, binding sites and…

PDB: 4YXQ
Type: protein
Length: 1,618 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg
EC: 2.3.3.-
UniProt: P40830
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-)	protein	407	38% helix, 26% strand	P40830
B	Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-)	protein	402	37% helix, 27% strand	P40830
D	Polyketide biosynthesis 3-hydroxy-3-methylglutaryl-acp synthase pksg (EC 2.3.3.-)	protein	402	37% helix, 26% strand	P40830

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D

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

Pockets

15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	561	0.79	0.85	55	empty
2	521	0.78	0.85	55	empty
3	423	0.76	0.85	47	empty
4	433	0.76	0.85	49	empty
5	1191	0.76	0.78	87	empty

Interfaces

5 interfaces between chains.

C–D · 3060 Å² buried · 59 hydrogen bonds · protein-protein
A–B · 3052 Å² buried · 60 hydrogen bonds · protein-protein
A–C · 846 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 249 Å² buried · 1 hydrogen bond · protein-protein
B–C · 244 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4YXQ · PksG, a HMG-CoA Synthase from Bacillus subtilis · the same entry in another collection · chain B against B, TM-score 1.00
P40830 · AlphaFold monomer V2.0 prediction for polyketide biosynthesis… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P40830
Elsewhere: RCSB PDB 4YXQ · PDBe 4YXQ · UniProt P40830

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.