Research workbench
Entf, a terminal nonribosomal peptide synthetase module bound to the mbth-like protein ybdz
Analyse Entf, a terminal nonribosomal peptide synthetase module bound to the mbth-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JA1
- Type
- protein
- Length
- 1,297 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterobactin synthase component F; Enterobactin biosynthesis protein ybdz
- EC
- 2.7.7.-
- UniProt
- P11454, P18393
- Ligands
- 75C, CL
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterobactin synthase component F (EC 2.7.7.-) | protein | 1231 | 35% helix, 21% strand | P11454 |
| B | Enterobactin biosynthesis protein ybdz | protein | 66 | 21% helix, 26% strand | P18393 |
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
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.83 | 0.84 | 103 | 75C, CL |
| 2 | 1089 | 0.77 | 0.79 | 83 | empty |
| 3 | 225 | 0.62 | 0.82 | 25 | empty |
| 4 | 460 | 0.61 | 0.75 | 48 | empty |
| 5 | 250 | 0.59 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1468 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5JA1 · EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P18393 · AlphaFold monomer V2.0 prediction for enterobactin biosynthesis protein ybdz (P18393) · a predicted model of the same protein · chain B against A, TM-score 0.87
- 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 P18393
- Elsewhere: RCSB PDB 5JA1 · PDBe 5JA1 · UniProt P11454 · UniProt P18393
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