MolNFT v1 · #27592 · protein
The structure of the oligopeptide-binding protein, appa, from bacillus subtilis in complex with a nonapeptide.
1XOC · Oligopeptide-binding protein appa: “The structure of the oligopeptide-binding protein, appa, from bacillus subtilis in complex with a nonapeptide.”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 1XOC
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligopeptide-binding protein appa; Nonapeptide vdskntssw
- UniProt
- P42061
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligopeptide-binding protein appa | protein | 504 | 31% helix, 24% strand | P42061 |
| B | Nonapeptide vdskntssw | protein | 9 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 15 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.81 | 0.97 | 35 | ZN |
| 2 | 75 | 0.74 | 0.97 | 23 | empty |
| 3 | 129 | 0.49 | 0.79 | 21 | empty |
| 4 | 94 | 0.40 | 0.77 | 20 | ZN |
| 5 | 98 | 0.33 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1XOC · The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in… · the same entry in another collection · chain A against A, TM-score 1.00
- P42061 · AlphaFold monomer V2.0 prediction for oligopeptide-binding protein appa (P42061) · 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 P42061
- Elsewhere: RCSB PDB 1XOC · PDBe 1XOC · UniProt P42061
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