Research workbench
5'-nucleotidase (E. COLI) with an engineered disulfide bridge (S228C, P513C)
Analyse 5'-nucleotidase (E. COLI) with an engineered disulfide bridge (S228C, P513C) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OID
- Type
- protein
- Length
- 1,048 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein usha
- EC
- 3.1.3.5, 3.6.1.45
- UniProt
- P07024
- Ligands
- NI
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein usha (EC 3.1.3.5, 3.6.1.45) | protein | 525 | 30% helix, 30% strand | P07024 |
| B | Protein usha (EC 3.1.3.5, 3.6.1.45) | protein | 523 | 28% helix, 29% strand | P07024 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.81 | 0.82 | 90 | empty |
| 2 | 1174 | 0.75 | 0.77 | 115 | empty |
| 3 | 548 | 0.65 | 0.76 | 68 | empty |
| 4 | 279 | 0.58 | 0.78 | 30 | empty |
| 5 | 225 | 0.54 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 777 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1OID · 5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C) · the same entry in another collection · chain A against A, TM-score 1.00
- P07024 · AlphaFold monomer V2.0 prediction for protein usha (P07024) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 P07024
- Elsewhere: RCSB PDB 1OID · PDBe 1OID · UniProt P07024
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