Research workbench
Crystal structure of the enterobactin esterase fes from shigella flexneri in the presence of 2,3-di-hydroxy-N- benzoyl-glycine
Analyse Crystal structure of the enterobactin esterase fes from shigella flexneri in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C8D
- Type
- protein
- Length
- 1,514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enterochelin esterase
- UniProt
- Q83SB9
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enterochelin esterase | protein | 378 | 31% helix, 25% strand | Q83SB9 |
| B | Enterochelin esterase | protein | 379 | 32% helix, 26% strand | Q83SB9 |
| C | Enterochelin esterase | protein | 379 | 31% helix, 25% strand | Q83SB9 |
| D | Enterochelin esterase | protein | 378 | 31% helix, 26% strand | Q83SB9 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.81 | 0.83 | 74 | CIT |
| 2 | 1032 | 0.81 | 0.82 | 94 | CIT |
| 3 | 1136 | 0.81 | 0.82 | 79 | CIT |
| 4 | 1000 | 0.81 | 0.82 | 66 | CIT |
| 5 | 717 | 0.71 | 0.78 | 54 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1879 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1747 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 309 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3C8D · Crystal structure of the enterobactin esterase FES from Shigella flexneri in the presence… · the same entry in another collection · 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 Q83SB9
- Elsewhere: RCSB PDB 3C8D · PDBe 3C8D · UniProt Q83SB9
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