MolNFT v1 · #139605 · protein

Klebsiella pneumoniae ureg in complex with gmppnp and nickel

5XKT · Urease accessory protein ureg: “Klebsiella pneumoniae ureg in complex with gmppnp and nickel”. X-ray diffraction, 2 ligands (GNP, NI), 3 pockets (best druggability 0.69). MolNFT v1 #139605 on GenesisL1: 3D structure, binding sites…

PDB: 5XKT
Type: protein
Length: 398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urease accessory protein ureg
UniProt: R4YE37
Ligands: GNP, NI
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Urease accessory protein ureg	protein	199	43% helix, 20% strand	R4YE37

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 3 copies · chains A, B

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

Pockets

3 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	294	0.69	0.84	42	GNP, NI
2	321	0.66	0.81	42	GNP
3	59	0.46	0.84	26	empty

Interfaces

1 interface between chains.

A–B · 1315 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5XKT · Klebsiella pneumoniae UreG in complex with GMPPNP and nickel · the same entry in another collection · chain A against A, 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 R4YE37
Elsewhere: RCSB PDB 5XKT · PDBe 5XKT · UniProt R4YE37

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