MolNFT v1 · #12472 · protein

Adenylate kinase from methanococcus voltae

1KHT: “Adenylate kinase from methanococcus voltae”. X-ray diffraction, 1 ligand (AMP), 4 pockets (best druggability 0.75). MolNFT v1 #12472 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KHT
Type: protein
Length: 572 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: P43411
Ligands: AMP
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	190	51% helix, 17% strand	P43411
B, C	Adenylate kinase (EC 2.7.4.3)	protein	191	52% helix, 18% strand	P43411

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 2 copies · chains B, C

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

Pockets

4 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	527	0.75	0.83	59	AMP
2	406	0.73	0.84	53	AMP
3	362	0.58	0.76	37	empty
4	137	0.43	0.76	31	empty

Interfaces

3 interfaces between chains.

A–C · 882 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 846 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 817 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1KHT · Adenylate kinase from Methanococcus voltae · the same entry in another collection · chain A against A, TM-score 1.00
P43411 · AlphaFold monomer V2.0 prediction for adenylate kinase (P43411) · 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 P43411
Elsewhere: RCSB PDB 1KHT · PDBe 1KHT · UniProt P43411

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