MolNFT v1 · #135307 · protein

A. aeolicus biow with AMP and CoA

5TVA · 6-carboxyhexanoate--CoA ligase: “A. aeolicus biow with AMP and CoA”. X-ray diffraction, 2 ligands (AMP, COA), 6 pockets (best druggability 0.75). MolNFT v1 #135307 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TVA
Type: protein
Length: 477 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 6-carboxyhexanoate--CoA ligase
EC: 6.2.1.14
UniProt: O67575
Ligands: AMP, COA
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	6-carboxyhexanoate--CoA ligase (EC 6.2.1.14)	protein	239	32% helix, 31% strand	O67575
B	6-carboxyhexanoate--CoA ligase (EC 6.2.1.14)	protein	238	32% helix, 31% strand	O67575

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
COA · Coenzyme A · ligand · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	701	0.75	0.81	46	AMP, COA
2	598	0.67	0.77	45	AMP
3	222	0.48	0.74	30	empty
4	115	0.38	0.74	21	empty
5	101	0.37	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 82 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5TVA · A. aeolicus BioW with AMP and CoA · the same entry in another collection · chain A against A, TM-score 1.00
O67575 · AlphaFold monomer V2.0 prediction for 6-carboxyhexanoate--CoA ligase (O67575) · 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 O67575
Elsewhere: RCSB PDB 5TVA · PDBe 5TVA · UniProt O67575

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