MolNFT v1 · #61056 · protein
Crystallographic structure of D-amino acid aminotransferase inactivated by pyridoxyl-D-alanine
3DAA: “Crystallographic structure of D-amino acid aminotransferase inactivated by pyridoxyl-D-alanine”. X-ray diffraction, 1 ligand (PDD), 4 pockets (best druggability 0.83). MolNFT v1 #61056 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DAA
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-amino acid aminotransferase
- EC
- 2.6.1.21
- UniProt
- P19938
- Ligands
- PDD
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | D-amino acid aminotransferase (EC 2.6.1.21) | protein | 277 | 30% helix, 31% strand | P19938 |
Ligands and binding sites
- PDD · N-(5'-phosphopyridoxyl)-D-alanine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.83 | 0.85 | 110 | PDD |
| 2 | 53 | 0.34 | 0.78 | 12 | empty |
| 3 | 70 | 0.34 | 0.76 | 19 | empty |
| 4 | 53 | 0.33 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2303 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3DAA · Crystallographic structure of D-amino acid aminotransferase inactivated by… · the same entry in another collection · chain B against B, TM-score 1.00
- P19938 · AlphaFold monomer V2.0 prediction for D-alanine aminotransferase (P19938) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P19938
- Elsewhere: RCSB PDB 3DAA · PDBe 3DAA · UniProt P19938
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