Research workbench
Crystal structure of phosphohydrolase (BT4208) from bacteroides thetaiotaomicron vpi-5482 at 2.20 a resolution
Analyse Crystal structure of phosphohydrolase (BT4208) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q14
- Type
- protein
- Length
- 3,216 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphohydrolase
- UniProt
- Q8A013
- Ligands
- ADP, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Phosphohydrolase | protein | 403 | 56% helix, 12% strand | Q8A013 |
| B, F | Phosphohydrolase | protein | 400 | 56% helix, 10% strand | Q8A013 |
| C | Phosphohydrolase | protein | 406 | 55% helix, 12% strand | Q8A013 |
| D | Phosphohydrolase | protein | 403 | 55% helix, 10% strand | Q8A013 |
| H | Phosphohydrolase | protein | 398 | 57% helix, 10% strand | Q8A013 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, D, C, E, F, H, G
- CL · Chloride ion · ion · 3 copies · chains A, D, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, E, G
- GOL · Glycerol · additive · 3 copies · chains B, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.88 | 0.89 | 157 | ADP |
| 2 | 1024 | 0.86 | 0.87 | 119 | ADP |
| 3 | 466 | 0.85 | 0.92 | 74 | ADP |
| 4 | 1187 | 0.83 | 0.84 | 138 | ADP |
| 5 | 803 | 0.83 | 0.85 | 96 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1652 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1648 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1616 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1608 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1383 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 98 modified (engineered).
Compared structures
- 2Q14 · Crystal structure of Phosphohydrolase (BT4208) from Bacteroides thetaiotaomicron VPI-5482… · the same entry in another collection · chain G against G, 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 Q8A013
- Elsewhere: RCSB PDB 2Q14 · PDBe 2Q14 · UniProt Q8A013
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