MolNFT v1 · #149467 · protein
Crystal structure of D-phenylglycine aninotransferase (D-phgat) from pseudomonas stutzeri with plp internal aldimine
6G1F · D-phenylglycine aminotransferase: “Crystal structure of D-phenylglycine aninotransferase (D-phgat) from pseudomonas stutzeri with plp internal…”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #149467 on…
- PDB
- 6G1F
- Type
- protein
- Length
- 2,641 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-phenylglycine aminotransferase
- UniProt
- Q6VY99
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-phenylglycine aminotransferase | protein | 443 | 45% helix, 16% strand | Q6VY99 |
| B, D | D-phenylglycine aminotransferase | protein | 441 | 44% helix, 17% strand | Q6VY99 |
| C | D-phenylglycine aminotransferase | protein | 440 | 44% helix, 17% strand | Q6VY99 |
| E | D-phenylglycine aminotransferase | protein | 438 | 43% helix, 17% strand | Q6VY99 |
| F | D-phenylglycine aminotransferase | protein | 438 | 44% helix, 17% strand | Q6VY99 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.78 | 0.82 | 75 | empty |
| 2 | 846 | 0.78 | 0.81 | 83 | empty |
| 3 | 852 | 0.77 | 0.80 | 82 | empty |
| 4 | 765 | 0.76 | 0.80 | 84 | empty |
| 5 | 788 | 0.75 | 0.80 | 80 | empty |
Interfaces
8 interfaces between chains.
- B–D · 5016 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 4992 Ų buried · 69 hydrogen bonds · protein-protein
- E–F · 4949 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 351 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor).
Compared structures
- 6G1F · Crystal structure of D-phenylglycine aninotransferase (D-PhgAT) from Pseudomonas stutzeri… · 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 6G1F · PDBe 6G1F · UniProt Q6VY99
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