Research workbench
Pvdf of pyoverdin biosynthesis is a structurally unique N10- formyltetrahydrofolate-dependent formyltransferase
Analyse Pvdf of pyoverdin biosynthesis is a structurally unique N10… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CUL
- Type
- protein
- Length
- 2,117 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyoverdine synthetase F
- UniProt
- Q9I184
- Ligands
- FGD
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyoverdine synthetase F | protein | 267 | 32% helix, 22% strand | Q9I184 |
| B | Pyoverdine synthetase F | protein | 263 | 34% helix, 23% strand | Q9I184 |
| D | Pyoverdine synthetase F | protein | 267 | 34% helix, 24% strand | Q9I184 |
| E | Pyoverdine synthetase F | protein | 264 | 33% helix, 24% strand | Q9I184 |
| F | Pyoverdine synthetase F | protein | 257 | 35% helix, 23% strand | Q9I184 |
| G | Pyoverdine synthetase F | protein | 265 | 35% helix, 26% strand | Q9I184 |
| H | Pyoverdine synthetase F | protein | 267 | 34% helix, 22% strand | Q9I184 |
Ligands and binding sites
- FGD · N-(4-{[(2-amino-4-oxo-1,4-dihydroquinazolin-6-yl) methyl]amino}benzene-1-carbonyl)-D-glutamic acid · ligand · 7 copies · chains A, B, C, D, E, H, F, G
- CIT · Citric acid · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.79 | 0.81 | 91 | FGD, CIT |
| 2 | 964 | 0.79 | 0.81 | 91 | FGD |
| 3 | 868 | 0.79 | 0.81 | 89 | CIT |
| 4 | 901 | 0.77 | 0.80 | 89 | FGD, CIT |
| 5 | 845 | 0.76 | 0.80 | 86 | FGD, CIT |
Interfaces
12 interfaces between chains.
- F–G · 830 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 800 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 795 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 795 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 773 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 6CUL · PvdF of pyoverdin biosynthesis is a structurally unique… · 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 Q9I184
- Elsewhere: RCSB PDB 6CUL · PDBe 6CUL · UniProt Q9I184
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