MolNFT v1 · #103717 · protein
Structure of the pbp noct in complex with pyronopaline
4POW · Nopaline-binding periplasmic protein: “Structure of the pbp noct in complex with pyronopaline”. X-ray diffraction, 1 ligand (OP1), 5 pockets (best druggability 0.73). MolNFT v1 #103717 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4POW
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nopaline-binding periplasmic protein
- UniProt
- P35120
- Ligands
- OP1
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nopaline-binding periplasmic protein | protein | 254 | 41% helix, 23% strand | P35120 |
Ligands and binding sites
- OP1 · 1-[(1S)-4-carbamimidamido-1-carboxybutyl]-5-oxo-D-proline · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.73 | 0.95 | 29 | OP1 |
| 2 | 109 | 0.73 | 0.94 | 29 | OP1 |
| 3 | 773 | 0.70 | 0.77 | 54 | empty |
| 4 | 53 | 0.28 | 0.75 | 13 | empty |
| 5 | 51 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4POW · Structure of the PBP NocT in complex with pyronopaline · the same entry in another collection · chain A against A, TM-score 1.00
- P35120 · AlphaFold monomer V2.0 prediction for nopaline-binding periplasmic protein (P35120) · 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 P35120
- Elsewhere: RCSB PDB 4POW · PDBe 4POW · UniProt P35120
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