Research workbench
Oligo-peptide binding protein (oppa) complexed with kgk
Analyse Oligo-peptide binding protein (oppa) complexed with kgk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B3L
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (oligo-peptide binding protein); Protein (lys-gly-lys)
- UniProt
- P06202
- Ligands
- IUM
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein (oligo-peptide binding protein) | protein | 517 | 35% helix, 22% strand | P06202 |
| B, D | Protein (lys-gly-lys) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.61 | 0.92 | 19 | empty |
| 2 | 252 | 0.49 | 0.74 | 28 | empty |
| 3 | 103 | 0.43 | 0.78 | 22 | empty |
| 4 | 120 | 0.43 | 0.77 | 21 | empty |
| 5 | 53 | 0.39 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 442 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 439 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1B3L · Oligo-peptide binding protein (oppa) complexed with kgk · 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 1B3L · PDBe 1B3L · UniProt P06202
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