MolNFT v1 · #92417 · protein
Crystal structure of pigeon pea urease
4G7E: “Crystal structure of pigeon pea urease”. X-ray diffraction, 2 ligands (NI, MG), 8 pockets (best druggability 0.73). MolNFT v1 #92417 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4G7E
- Type
- protein
- Length
- 1,666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease
- EC
- 3.5.1.5
- Ligands
- NI, MG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease (EC 3.5.1.5) | protein | 833 | 30% helix, 23% strand | — |
| B | Urease (EC 3.5.1.5) | protein | 833 | 30% helix, 23% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.73 | 0.79 | 79 | empty |
| 2 | 913 | 0.72 | 0.76 | 99 | empty |
| 3 | 862 | 0.71 | 0.76 | 95 | empty |
| 4 | 150 | 0.51 | 0.79 | 19 | empty |
| 5 | 128 | 0.44 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 896 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (artifact, carboxylation).
Compared structures
- 4G7E · Crystal structure of pigeon pea urease · 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
- Elsewhere: RCSB PDB 4G7E · PDBe 4G7E
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