MolNFT v1 · #180053 · protein

Cryo-EM structure of jack bean urease

7KNS: “Cryo-EM structure of jack bean urease”. Electron microscopy, 2 ligands (NI, PO4), 20 pockets (best druggability 0.83). MolNFT v1 #180053 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7KNS
Type: protein
Length: 5,022 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Urease
EC: 3.5.1.5
UniProt: P07374
Ligands: NI, PO4
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 1 distinct chain · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Urease (EC 3.5.1.5)	protein	837	28% helix, 23% strand	P07374

Ligands and binding sites

NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	262	0.83	0.95	38	empty
2	624	0.83	0.88	69	empty
3	550	0.82	0.88	80	empty
4	660	0.82	0.87	95	empty
5	503	0.82	0.89	81	empty

Interfaces

15 interfaces between chains.

E–F · 5133 Å² buried · 88 hydrogen bonds · protein-protein
A–B · 5132 Å² buried · 87 hydrogen bonds · protein-protein
D–E · 5127 Å² buried · 94 hydrogen bonds · protein-protein
B–C · 5102 Å² buried · 88 hydrogen bonds · protein-protein
A–C · 5101 Å² buried · 92 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (carboxylation).

Compared structures

7KNS · Cryo-EM structure of jack bean urease · the same entry in another collection · chain C against C, TM-score 1.00
P07374 · AlphaFold monomer V2.0 prediction for urease (P07374) · 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 P07374
Elsewhere: RCSB PDB 7KNS · PDBe 7KNS · UniProt P07374

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