Research workbench
Crystal structure of aminotransferase class I and II from veillonella parvula
Analyse Crystal structure of aminotransferase class I and II from veillonella parvula in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RQ1
- Type
- protein
- Length
- 1,633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class I and II
- UniProt
- D1BN29
- Ligands
- OAA, AKG, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminotransferase class I and II | protein | 414 | 49% helix, 16% strand | D1BN29 |
| C | Aminotransferase class I and II | protein | 413 | 47% helix, 16% strand | D1BN29 |
| D | Aminotransferase class I and II | protein | 392 | 46% helix, 17% strand | D1BN29 |
Ligands and binding sites
- OAA · Oxaloacetate ion · ligand · 3 copies · chains A, C, B, D
- AKG · 2-oxoglutaric acid · ligand · chains A, C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 10 copies · chains A, C, B, D
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 | 123 | 0.77 | 0.96 | 25 | OAA, GOL |
| 2 | 113 | 0.75 | 0.95 | 27 | GOL |
| 3 | 61 | 0.74 | 0.99 | 17 | empty |
| 4 | 55 | 0.73 | 0.99 | 16 | empty |
| 5 | 81 | 0.72 | 0.96 | 22 | OAA |
Interfaces
3 interfaces between chains.
- A–C · 3406 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 3403 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3RQ1 · Crystal Structure of Aminotransferase Class I and II from Veillonella parvula · 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 D1BN29
- Elsewhere: RCSB PDB 3RQ1 · PDBe 3RQ1 · UniProt D1BN29
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