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Crystal structure of anmk bound to amppcp

Analyse Crystal structure of anmk bound to amppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MO4
Type: protein
Length: 1,400 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anhydro-N-acetylmuramic acid kinase
EC: 2.7.1.170
UniProt: Q9I5Q5
Ligands: ACP
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Anhydro-N-acetylmuramic acid kinase (EC 2.7.1.170)	protein	345	46% helix, 22% strand	Q9I5Q5
B	Anhydro-N-acetylmuramic acid kinase (EC 2.7.1.170)	protein	348	47% helix, 22% strand	Q9I5Q5
C	Anhydro-N-acetylmuramic acid kinase (EC 2.7.1.170)	protein	354	45% helix, 21% strand	Q9I5Q5
D	Anhydro-N-acetylmuramic acid kinase (EC 2.7.1.170)	protein	353	45% helix, 22% strand	Q9I5Q5

Ligands and binding sites

ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D

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

Pockets

12 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	371	0.85	0.94	53	empty
2	893	0.84	0.86	125	empty
3	394	0.68	0.81	59	ACP
4	374	0.57	0.75	45	empty
5	369	0.56	0.75	45	empty

Interfaces

5 interfaces between chains.

A–B · 1666 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 1658 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 581 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 229 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 126 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4MO4 · Crystal structure of AnmK bound to AMPPCP · the same entry in another collection · chain D against D, TM-score 1.00
Q9I5Q5 · AlphaFold monomer V2.0 prediction for anhydro-N-acetylmuramic acid kinase (Q9I5Q5) · a predicted model of the same protein · chain B 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 Q9I5Q5
Elsewhere: RCSB PDB 4MO4 · PDBe 4MO4 · UniProt Q9I5Q5

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