MolNFT v1 · #171866 · protein

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor GP5A

6ZJB · GTP:AMP phosphotransferase AK3, mitochondrial: “Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor GP5A”. X-ray diffraction, 2 ligands (G5P, MG), 15 pockets (best druggability 0.81). MolNFT v1 #171866 on…

PDB: 6ZJB
Type: protein
Length: 1,300 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GTP:AMP phosphotransferase AK3, mitochondrial
EC: 2.7.4.10
UniProt: Q9UIJ7
Ligands: G5P, MG
Pockets: 15 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10)	protein	217	48% helix, 17% strand	Q9UIJ7
C	GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10)	protein	216	49% helix, 17% strand	Q9UIJ7
D	GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10)	protein	218	48% helix, 18% strand	Q9UIJ7
E, F	GTP:AMP phosphotransferase AK3, mitochondrial (EC 2.7.4.10)	protein	216	48% helix, 17% strand	Q9UIJ7

Ligands and binding sites

G5P · P1-(5'-adenosyl)-P5-(5'-guanosyl) pentaphosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	451	0.81	0.89	51	G5P, MG
2	469	0.80	0.88	52	G5P, MG
3	473	0.80	0.88	53	G5P, MG
4	630	0.79	0.85	58	G5P, MG
5	542	0.78	0.85	63	G5P, MG

Interfaces

7 interfaces between chains.

B–D · 614 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 566 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 540 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 309 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 142 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6ZJB · Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A · the same entry in another collection · chain B against B, TM-score 1.00
Q9UIJ7 · AlphaFold monomer V2.0 prediction for GTP:AMP phosphotransferase AK3, mitochondrial… · a predicted model of the same protein · chain E against A, TM-score 0.97

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 Q9UIJ7
Elsewhere: RCSB PDB 6ZJB · PDBe 6ZJB · UniProt Q9UIJ7

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