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Structures of P. aeruginosa fpva bound to heterologous pyoverdines: fpva-PVD(DSM50106)-fe complex
Analyse Structures of P. aeruginosa fpva bound to heterologous pyoverdines… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W6T
- Type
- protein
- Length
- 1,536 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferripyoverdine receptor; Pyoverdine
- UniProt
- P48632
- Ligands
- N8E, PVE, FE, PO4
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferripyoverdine receptor | protein | 772 | 8% helix, 55% strand | P48632 |
| B | Ferripyoverdine receptor | protein | 754 | 8% helix, 55% strand | P48632 |
| C | Pyoverdine | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- N8E · 3,6,9,12,15-pentaoxatricosan-1-ol · ligand · 2 copies · chains A, B
- PVE · (1S)-1-carboxy-5-[(3-carboxypropanoyl)amino]-8,9-dihydroxy-1,2,3,4-tetrahydropyrimido[1,2-a]quinolin-11-ium · ligand · chains B, C
- FE · Fe (III) ion · metal · chains B, C
- PO4 · Phosphate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.86 | 0.92 | 65 | PO4 |
| 2 | 1000 | 0.84 | 0.85 | 136 | PO4 |
| 3 | 1133 | 0.81 | 0.83 | 85 | PVE |
| 4 | 290 | 0.78 | 0.90 | 50 | empty |
| 5 | 797 | 0.77 | 0.81 | 108 | PO4 |
Interfaces
2 interfaces between chains.
- A–B · 646 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 616 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 2 d-amino, 1 covalent (nonstandard, D-amino acid, covalent ligand).
Compared structures
- 2W6T · Structures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(DSM50106)-Fe… · the same entry in another collection · chain A against A, TM-score 1.00
- P48632 · AlphaFold monomer V2.0 prediction for ferripyoverdine receptor (P48632) · a predicted model of the same protein · 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 P48632
- Elsewhere: RCSB PDB 2W6T · PDBe 2W6T · UniProt P48632
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