MolNFT v1 · #178532 · protein

Kpacka (pduw) with AMP complex structure

7FJ8 · Probable propionate kinase: “Kpacka (pduw) with AMP complex structure”. X-ray diffraction, 1 ligand (AMP), 5 pockets (best druggability 0.85). MolNFT v1 #178532 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7FJ8
Type: protein
Length: 737 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable propionate kinase
EC: 2.7.2.15
UniProt: A0A0H3GUQ7
Ligands: AMP
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable propionate kinase (EC 2.7.2.15)	protein	395	43% helix, 22% strand	A0A0H3GUQ7
B	Probable propionate kinase (EC 2.7.2.15)	protein	342	43% helix, 17% strand	A0A0H3GUQ7

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.85	0.94	53	empty
2	460	0.64	0.77	49	empty
3	438	0.62	0.76	53	empty
4	71	0.45	0.82	17	empty
5	70	0.40	0.79	18	empty

Interfaces

1 interface between chains.

A–B · 3057 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7FJ8 · KpAckA (PduW) with AMP complex structure · 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 A0A0H3GUQ7
Elsewhere: RCSB PDB 7FJ8 · PDBe 7FJ8 · UniProt A0A0H3GUQ7

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