MolNFT v1 · #1553 · protein
Oligo-peptide binding protein (oppa) complexed with kyk
1B58 · Protein (oligo-peptide binding protein): “Oligo-peptide binding protein (oppa) complexed with kyk”. X-ray diffraction, 1 ligand (IUM), 4 pockets (best druggability 0.41). MolNFT v1 #1553 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1B58
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (oligo-peptide binding protein); Protein (lys-tyr-lys)
- UniProt
- P06202
- Ligands
- IUM
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (oligo-peptide binding protein) | protein | 517 | 35% helix, 22% strand | P06202 |
| B | Protein (lys-tyr-lys) | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- IUM · Uranyl (VI) ion · metal · 8 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 0.41 | 0.76 | 23 | empty |
| 2 | 52 | 0.39 | 0.81 | 16 | empty |
| 3 | 65 | 0.31 | 0.75 | 18 | empty |
| 4 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1B58 · Oligo-peptide binding protein (oppa) complexed with kyk · 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 1B58 · PDBe 1B58 · UniProt P06202
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