MolNFT v1 · #152442 · protein

Structure of mmpa CoA ligase in complex with ADP

6IHK · AMP-binding domain protein: “Structure of mmpa CoA ligase in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 8 pockets (best druggability 0.81). MolNFT v1 #152442 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6IHK
Type: protein
Length: 1,059 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: AMP-binding domain protein
UniProt: D0CPY8
Ligands: ADP
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	AMP-binding domain protein	protein	526	34% helix, 26% strand	D0CPY8
B	AMP-binding domain protein	protein	533	33% helix, 26% strand	D0CPY8

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains B

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	880	0.81	0.83	95	ADP
2	533	0.62	0.75	62	empty
3	452	0.60	0.75	75	empty
4	199	0.53	0.78	29	empty
5	214	0.50	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 271 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6IHK · Structure of MMPA CoA ligase in complex with ADP · the same entry in another collection · 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 D0CPY8
Elsewhere: RCSB PDB 6IHK · PDBe 6IHK · UniProt D0CPY8

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