Research workbench
Pyoverdine outer membrane receptor fpva from pseudomonas aeruginosa PAO1 bound to pyoverdine
Analyse Pyoverdine outer membrane receptor fpva from pseudomonas aeruginosa PAO1 bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XKH
- Type
- protein
- Length
- 2,085 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferripyoverdine receptor; Pyoverdin C-E
- UniProt
- P48632
- Ligands
- PVE, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ferripyoverdine receptor | protein | 687 | 3% helix, 50% strand | P48632 |
| I, J, K | Pyoverdin C-E | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- PVE · (1S)-1-carboxy-5-[(3-carboxypropanoyl)amino]-8,9-dihydroxy-1,2,3,4-tetrahydropyrimido[1,2-a]quinolin-11-ium · ligand · 3 copies · chains A, I, B, J, C, K
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.86 | 0.90 | 109 | empty |
| 2 | 664 | 0.85 | 0.90 | 100 | empty |
| 3 | 709 | 0.85 | 0.89 | 99 | empty |
| 4 | 1083 | 0.84 | 0.85 | 88 | PVE |
| 5 | 183 | 0.80 | 0.96 | 48 | empty |
Interfaces
3 interfaces between chains.
- C–K · 662 Ų buried · 9 hydrogen bonds · protein-protein
- B–J · 630 Ų buried · 9 hydrogen bonds · protein-protein
- A–I · 624 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified, 6 d-amino, 3 covalent, 3 isopeptide (engineered, D-amino acid, nonstandard, covalent ligand, isopeptide).
Compared structures
- 1XKH · Pyoverdine outer membrane receptor FpvA from Pseudomonas aeruginosa PAO1 bound to… · the same entry in another collection · chain K against K, TM-score 1.00
- P48632 · AlphaFold monomer V2.0 prediction for ferripyoverdine receptor (P48632) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 1XKH · PDBe 1XKH · UniProt P48632
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