Research workbench
Crystal structure of putative exopolyphosphatase (17739545) from agrobacterium tumefaciens str. C58 (dupont) at 2.30 a resolution
Analyse Crystal structure of putative exopolyphosphatase (17739545) from agrobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HI0
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exopolyphosphatase
- UniProt
- A9CJF9
- Ligands
- CL
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exopolyphosphatase | protein | 501 | 53% helix, 15% strand | A9CJF9 |
| B | Putative exopolyphosphatase | protein | 493 | 52% helix, 14% strand | A9CJF9 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.88 | 0.91 | 106 | MPD |
| 2 | 263 | 0.76 | 0.90 | 45 | empty |
| 3 | 286 | 0.75 | 0.88 | 51 | empty |
| 4 | 91 | 0.55 | 0.86 | 18 | empty |
| 5 | 94 | 0.45 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3244 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3HI0 · Crystal structure of Putative exopolyphosphatase (17739545) from AGROBACTERIUM… · 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 A9CJF9
- Elsewhere: RCSB PDB 3HI0 · PDBe 3HI0 · UniProt A9CJF9
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