MolNFT v1 · #134410 · protein
Crystal structure of holo-entf a nonribosomal peptide synthetase in the thioester-forming conformation
5T3D · Enterobactin synthase component F: “Crystal structure of holo-entf a nonribosomal peptide synthetase in the thioester-forming conformation”. X-ray diffraction, 1 ligand (75C), 11 pockets (best druggability 0.85). MolNFT v1 #134410…
- PDB
- 5T3D
- Type
- protein
- Length
- 1,042 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterobactin synthase component F
- EC
- 2.7.7.-
- UniProt
- P11454
- Ligands
- 75C
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterobactin synthase component F (EC 2.7.7.-) | protein | 1042 | 36% helix, 22% strand | P11454 |
Ligands and binding sites
- 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.85 | 0.86 | 90 | empty |
| 2 | 1047 | 0.83 | 0.84 | 101 | 75C |
| 3 | 287 | 0.56 | 0.77 | 33 | empty |
| 4 | 134 | 0.48 | 0.78 | 25 | empty |
| 5 | 176 | 0.46 | 0.75 | 26 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5T3D · Crystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming… · 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 0.93
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
- Elsewhere: RCSB PDB 5T3D · PDBe 5T3D · UniProt P11454
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