MolNFT v1 · #90638 · protein
Initial urease structure for radiation damage experiment at 100 K
4EP8 · Urease subunit alpha: “Initial urease structure for radiation damage experiment at 100 K”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.68). MolNFT v1 #90638 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4EP8
- Type
- protein
- Length
- 767 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease subunit alpha; Urease subunit beta; Urease subunit gamma
- EC
- 3.5.1.5
- UniProt
- P18314, P18315, P18316
- Ligands
- NI
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Urease subunit alpha (EC 3.5.1.5) | protein | 566 | 30% helix, 23% strand | P18314 |
| B | Urease subunit beta (EC 3.5.1.5) | protein | 101 | 3% helix, 38% strand | P18315 |
| A | Urease subunit gamma (EC 3.5.1.5) | protein | 100 | 56% helix, 18% strand | P18316 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.68 | 0.76 | 59 | empty |
| 2 | 171 | 0.45 | 0.75 | 31 | empty |
| 3 | 127 | 0.40 | 0.75 | 16 | empty |
| 4 | 69 | 0.39 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1813 Ų buried · 27 hydrogen bonds · protein-protein
- C–A · 970 Ų buried · 14 hydrogen bonds · protein-protein
- B–A · 163 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4EP8 · Initial Urease Structure for Radiation Damage Experiment at 100 K · the same entry in another collection · chain C against C, TM-score 1.00
- P18314 · AlphaFold monomer V2.0 prediction for urease subunit alpha (P18314) · a predicted model of the same protein · chain C against A, TM-score 1.00
- P18315 · AlphaFold monomer V2.0 prediction for urease subunit beta (P18315) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P18316 · AlphaFold monomer V2.0 prediction for urease subunit gamma (P18316) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P18314
- Every structure of UniProt P18315
- Every structure of UniProt P18316
- Elsewhere: RCSB PDB 4EP8 · PDBe 4EP8 · UniProt P18314 · UniProt P18315 · UniProt P18316
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