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Crystal structure of adenylate kinase from methanococcus maripaludis

Analyse Crystal structure of adenylate kinase from methanococcus maripaludis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H86
Type: protein
Length: 764 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: Q6LYG0
Ligands: AP5
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, G	Adenylate kinase (EC 2.7.4.3)	protein	191	46% helix, 17% strand	Q6LYG0

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 4 copies · chains B, A, C, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	587	0.79	0.85	48	AP5
2	485	0.77	0.85	52	AP5
3	427	0.77	0.86	45	AP5
4	451	0.75	0.84	49	AP5
5	450	0.62	0.76	49	empty

Interfaces

5 interfaces between chains.

B–C · 852 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 842 Å² buried · 8 hydrogen bonds · protein-protein
B–A · 837 Å² buried · 5 hydrogen bonds · protein-protein
A–G · 447 Å² buried · 3 hydrogen bonds · protein-protein
C–G · 42 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3H86 · Crystal structure of adenylate kinase from Methanococcus maripaludis · the same entry in another collection · chain B against B, TM-score 1.00
Q6LYG0 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q6LYG0) · a predicted model of the same protein · chain B against A, TM-score 0.88

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 Q6LYG0
Elsewhere: RCSB PDB 3H86 · PDBe 3H86 · UniProt Q6LYG0

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