Research workbench
Structure of the xanthomonas citri phosphate-binding protein phox
Analyse Structure of the xanthomonas citri phosphate-binding protein phox in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I84
- Type
- protein
- Length
- 2,506 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate-binding protein psts
- UniProt
- Q8PM55
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G | Phosphate-binding protein psts | protein | 314 | 40% helix, 17% strand | Q8PM55 |
| C | Phosphate-binding protein psts | protein | 312 | 41% helix, 19% strand | Q8PM55 |
| H | Phosphate-binding protein psts | protein | 310 | 37% helix, 19% strand | Q8PM55 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 34 copies · chains A, G, B, E, C, F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.81 | 0.83 | 80 | empty |
| 2 | 1031 | 0.81 | 0.83 | 71 | empty |
| 3 | 678 | 0.81 | 0.86 | 111 | PO4 |
| 4 | 602 | 0.77 | 0.83 | 57 | PO4 |
| 5 | 756 | 0.74 | 0.79 | 65 | PO4 |
Interfaces
16 interfaces between chains.
- C–E · 595 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 543 Ų buried · 2 hydrogen bonds · protein-protein
- A–G · 530 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 473 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 437 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5I84 · Structure of the Xanthomonas citri phosphate-binding protein PhoX · 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 Q8PM55
- Elsewhere: RCSB PDB 5I84 · PDBe 5I84 · UniProt Q8PM55
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