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Unliganded biosynthetic thiolase from zoogloea ramigera

Analyse Unliganded biosynthetic thiolase from zoogloea ramigera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DLU
Type: protein
Length: 1,556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biosynthetic thiolase
EC: 2.3.1.9
UniProt: P07097
Ligands: SO4
Pockets: 14 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Biosynthetic thiolase (EC 2.3.1.9)	protein	389	39% helix, 23% strand	P07097

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, C, D

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

Pockets

14 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	134	0.80	0.98	35	empty
2	117	0.79	0.98	32	empty
3	135	0.58	0.83	26	MPD
4	134	0.57	0.83	27	MPD
5	123	0.57	0.83	29	MPD

Interfaces

6 interfaces between chains.

A–B · 2628 Å² buried · 69 hydrogen bonds · protein-protein
C–D · 2623 Å² buried · 75 hydrogen bonds · protein-protein
B–C · 656 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 640 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 300 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1DLU · Unliganded biosynthetic thiolase from zoogloea ramigera · the same entry in another collection · chain A against A, TM-score 1.00
P07097 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P07097) · a predicted model of the same protein · chain A 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 P07097
Elsewhere: RCSB PDB 1DLU · PDBe 1DLU · UniProt P07097

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