MolNFT v1 · #34788 · protein
Crystal structure of the PH1308 protein from pyrococcus horikoshii OT3
2DR1 · 386AA long hypothetical serine aminotransferase: “Crystal structure of the PH1308 protein from pyrococcus horikoshii OT3”. X-ray diffraction, 3 ligands (PLP, NA, CL), 6 pockets (best druggability 0.70). MolNFT v1 #34788 on…
- PDB
- 2DR1
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 386AA long hypothetical serine aminotransferase
- UniProt
- O59033
- Ligands
- PLP, NA, CL
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 386AA long hypothetical serine aminotransferase | protein | 381 | 44% helix, 16% strand | O59033 |
| B | 386AA long hypothetical serine aminotransferase | protein | 374 | 44% helix, 17% strand | O59033 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.70 | 0.83 | 58 | CL, PLP |
| 2 | 312 | 0.69 | 0.83 | 45 | PLP, CL |
| 3 | 90 | 0.51 | 0.83 | 23 | empty |
| 4 | 99 | 0.48 | 0.81 | 24 | empty |
| 5 | 52 | 0.38 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3356 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2DR1 · Crystal structure of the PH1308 protein from Pyrococcus horikoshii OT3 · 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 O59033
- Elsewhere: RCSB PDB 2DR1 · PDBe 2DR1 · UniProt O59033
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