Research workbench
Phosphate binding protein
Analyse Phosphate binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OMB
- Type
- protein
- Length
- 1,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate binding protein
- UniProt
- Q9Z9M3
- Ligands
- PT, PO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphate binding protein | protein | 298 | 36% helix, 21% strand | Q9Z9M3 |
Ligands and binding sites
- PT · Platinum (II) ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.70 | 0.78 | 69 | empty |
| 2 | 593 | 0.70 | 0.78 | 64 | empty |
| 3 | 709 | 0.69 | 0.77 | 77 | empty |
| 4 | 140 | 0.59 | 0.84 | 21 | empty |
| 5 | 143 | 0.43 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1059 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 774 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 283 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4OMB · Phosphate binding protein · the same entry in another collection · chain C against C, 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 Q9Z9M3
- Elsewhere: RCSB PDB 4OMB · PDBe 4OMB · UniProt Q9Z9M3
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