MolNFT v1 · #180864 · protein

Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant

7LDC · Acetyl-CoA acetyltransferase: “Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant”. X-ray diffraction, 2 ligands (COA, SO4), 17 pockets (best druggability 0.79). MolNFT v1 #180864 on GenesisL1: 3D structure, binding sites…

PDB: 7LDC
Type: protein
Length: 1,553 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acetyl-CoA acetyltransferase
EC: 2.3.1.9
UniProt: P07097
Ligands: COA, SO4
Pockets: 17 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acetyl-CoA acetyltransferase (EC 2.3.1.9)	protein	390	39% helix, 24% strand	P07097
B	Acetyl-CoA acetyltransferase (EC 2.3.1.9)	protein	387	40% helix, 24% strand	P07097
C	Acetyl-CoA acetyltransferase (EC 2.3.1.9)	protein	389	40% helix, 24% strand	P07097
D	Acetyl-CoA acetyltransferase (EC 2.3.1.9)	protein	387	40% helix, 24% strand	P07097

Ligands and binding sites

COA · Coenzyme A · ligand · 4 copies · chains A, D, B, C
SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D

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

Pockets

17 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	109	0.79	0.98	36	empty
2	114	0.78	0.98	41	empty
3	237	0.59	0.79	35	COA
4	215	0.58	0.79	37	COA
5	207	0.57	0.79	38	COA

Interfaces

6 interfaces between chains.

C–D · 2656 Å² buried · 78 hydrogen bonds · protein-protein
A–B · 2653 Å² buried · 79 hydrogen bonds · protein-protein
B–C · 692 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 681 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 287 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (acetylation).

Compared structures

7LDC · Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E mutant · the same entry in another collection · chain D against D, TM-score 1.00
P07097 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P07097) · a predicted model of the same protein · chain C 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 7LDC · PDBe 7LDC · UniProt P07097

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