Research workbench
Structures of P. aeruginosa fpva bound to heterologous pyoverdines: fpva-PVD(PA6)-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
- 2W76
- Type
- protein
- Length
- 1,532 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferripyoverdine receptor; Pyoverdin R
- UniProt
- P48632
- Ligands
- N8E, DSN, PVE, FE, PO4
- Pockets
- 15 · 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 | 7% helix, 55% strand | P48632 |
| B | Ferripyoverdine receptor | protein | 754 | 7% helix, 55% strand | P48632 |
| C | Pyoverdin R | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- N8E · 3,6,9,12,15-pentaoxatricosan-1-ol · ligand · 2 copies · chains A, B
- DSN · D-serine · ligand · chains B, C
- 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
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.86 | 0.88 | 163 | PO4 |
| 2 | 468 | 0.85 | 0.93 | 66 | PO4 |
| 3 | 1070 | 0.80 | 0.82 | 82 | PVE |
| 4 | 1160 | 0.75 | 0.78 | 87 | empty |
| 5 | 423 | 0.75 | 0.85 | 62 | empty |
Interfaces
2 interfaces between chains.
- A–B · 651 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 462 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent, 1 d-amino (nonstandard, covalent ligand, D-amino acid).
Compared structures
- 2W76 · Structures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(Pa6)-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 2W76 · PDBe 2W76 · UniProt P48632
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.