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The structure of E. COLI ump kinase in complex with ump

Analyse The structure of E. COLI ump kinase in complex with ump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BNE
Type: protein
Length: 472 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridylate kinase
EC: 2.7.4.4
UniProt: P29464
Ligands: U5P
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uridylate kinase (EC 2.7.4.4)	protein	234	39% helix, 19% strand	P29464
B	Uridylate kinase (EC 2.7.4.4)	protein	238	38% helix, 18% strand	P29464

Ligands and binding sites

U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	281	0.62	0.80	42	U5P
2	232	0.60	0.80	42	U5P
3	105	0.41	0.76	25	empty
4	65	0.35	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 1246 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2BNE · The structure of E. coli UMP kinase in complex with UMP · the same entry in another collection · chain B against B, 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 P29464
Elsewhere: RCSB PDB 2BNE · PDBe 2BNE · UniProt P29464

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