Research workbench
Oligo-peptide binding protein (oppa) complexed with knk
Analyse Oligo-peptide binding protein (oppa) complexed with knk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B5I
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Salmonella typhimurium; SYNTHETIC CONSTRUCT
- Molecule
- Protein (oligo-peptide binding protein); Protein (lys-asn-lys)
- UniProt
- P06202
- Ligands
- U1
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (oligo-peptide binding protein) | protein | 517 | 34% helix, 22% strand | P06202 |
| B | Protein (lys-asn-lys) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- U1 · Uranium atom · metal · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.43 | 0.77 | 25 | empty |
| 2 | 81 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1B5I · Oligo-peptide binding protein (oppa) complexed with knk · the same entry in another collection · chain A against A, TM-score 1.00
- P06202 · AlphaFold monomer V2.0 prediction for periplasmic oligopeptide- binding protein (P06202) · a predicted model of the same protein · 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 P06202
- Elsewhere: RCSB PDB 1B5I · PDBe 1B5I · UniProt P06202
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