MolNFT v1 · #123113 · protein
Entf, a terminal nonribosomal peptide synthetase module bound to the non-native mbth-like protein PA2412
5JA2 · Enterobactin synthase component F: “Entf, a terminal nonribosomal peptide synthetase module bound to the non-native mbth-like protein PA2412”. X-ray diffraction, 2 ligands (BU9, 75C), 14 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5JA2
- Type
- protein
- Length
- 1,306 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterobactin synthase component F; Mbth-like protein PA2412
- EC
- 2.7.7.-
- UniProt
- P11454, Q9I169
- Ligands
- BU9, 75C
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterobactin synthase component F (EC 2.7.7.-) | protein | 1238 | 35% helix, 21% strand | P11454 |
| B | Mbth-like protein PA2412 | protein | 68 | 25% helix, 28% strand | Q9I169 |
Ligands and binding sites
- BU9 · Meso-2,3-Butanediol · ligand · 2 copies · chains A, B
- 75C · 5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.83 | 0.84 | 100 | 75C |
| 2 | 1141 | 0.76 | 0.78 | 87 | empty |
| 3 | 657 | 0.69 | 0.77 | 70 | empty |
| 4 | 341 | 0.69 | 0.82 | 42 | empty |
| 5 | 398 | 0.57 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1240 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5JA2 · EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the non-Native MbtH-Like… · the same entry in another collection · chain A against A, TM-score 1.00
- P11454 · AlphaFold monomer V2.0 prediction for enterobactin synthase component F (P11454) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P11454
- Every structure of UniProt Q9I169
- Elsewhere: RCSB PDB 5JA2 · PDBe 5JA2 · UniProt P11454 · UniProt Q9I169
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