Research workbench
Crystal structure of pseudomonas stutzeri D-phenylglycine aminotransferase
Analyse Crystal structure of pseudomonas stutzeri D-phenylglycine aminotransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DVS
- Type
- protein
- Length
- 397 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-phenylglycine aminotransferase
- EC
- 2.6.1.72
- UniProt
- Q6VY99
- Ligands
- SO4, PO4
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-phenylglycine aminotransferase (EC 2.6.1.72) | protein | 397 | 47% helix, 17% strand | Q6VY99 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.55 | 0.80 | 25 | empty |
| 2 | 181 | 0.51 | 0.78 | 26 | empty |
| 3 | 57 | 0.46 | 0.84 | 17 | EDO, ACT |
| 4 | 78 | 0.33 | 0.75 | 23 | empty |
| 5 | 56 | 0.33 | 0.77 | 15 | empty |
Compared structures
- 6DVS · Crystal structure of Pseudomonas stutzeri D-phenylglycine aminotransferase · 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 Q6VY99
- Elsewhere: RCSB PDB 6DVS · PDBe 6DVS · UniProt Q6VY99
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