MolNFT v1 · #84794 · protein
Methylaspartate ammonia lyase from clostridium tetanomorphum mutant L384A
3ZVI · Methylaspartate ammonia-lyase: “Methylaspartate ammonia lyase from clostridium tetanomorphum mutant L384A”. X-ray diffraction, 3 ligands (ROP, MG, CL), 6 pockets (best druggability 0.86). MolNFT v1 #84794 on GenesisL1: 3D structure…
- PDB
- 3ZVI
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylaspartate ammonia-lyase
- EC
- 4.3.1.2
- UniProt
- Q05514
- Ligands
- ROP, MG, CL
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methylaspartate ammonia-lyase (EC 4.3.1.2) | protein | 415 | 46% helix, 17% strand | Q05514 |
Ligands and binding sites
- ROP · Propionamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.86 | 0.92 | 49 | GOL |
| 2 | 672 | 0.75 | 0.81 | 69 | ROP |
| 3 | 495 | 0.73 | 0.82 | 58 | ROP |
| 4 | 51 | 0.47 | 0.86 | 17 | GOL |
| 5 | 145 | 0.44 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2532 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3ZVI · Methylaspartate ammonia lyase from Clostridium tetanomorphum mutant L384A · the same entry in another collection · chain A against A, TM-score 1.00
- Q05514 · AlphaFold monomer V2.0 prediction for methylaspartate ammonia-lyase (Q05514) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q05514
- Elsewhere: RCSB PDB 3ZVI · PDBe 3ZVI · UniProt Q05514
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