Research workbench
Crystal structure of putative aspartate aminotransferase (NP_905498.1) from porphyromonas gingivalis W83 at 1.75 a resolution
Analyse Crystal structure of putative aspartate aminotransferase (NP_905498.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G0T
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aminotransferase
- UniProt
- Q7MUZ3
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aminotransferase | protein | 437 | 47% helix, 14% strand | Q7MUZ3 |
| B | Putative aminotransferase | protein | 435 | 47% helix, 14% strand | Q7MUZ3 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.77 | 0.82 | 64 | EDO |
| 2 | 626 | 0.75 | 0.82 | 53 | EDO |
| 3 | 94 | 0.36 | 0.75 | 22 | empty |
| 4 | 52 | 0.32 | 0.77 | 19 | empty |
| 5 | 76 | 0.30 | 0.73 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 2238 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified (engineered, cofactor).
Compared structures
- 3G0T · Crystal structure of putative aspartate aminotransferase (NP_905498.1) from Porphyromonas… · 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 Q7MUZ3
- Elsewhere: RCSB PDB 3G0T · PDBe 3G0T · UniProt Q7MUZ3
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