MolNFT v1 · #12311 · protein
Crystal structure of beta-methylaspartase from clostridium tetanomorphum. apo-structure.
1KD0: “Crystal structure of beta-methylaspartase from clostridium tetanomorphum. apo-structure.”. X-ray diffraction, 5 pockets (best druggability 0.87). MolNFT v1 #12311 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KD0
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-methylaspartase
- EC
- 4.3.1.2
- UniProt
- Q05514
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-methylaspartase (EC 4.3.1.2) | protein | 413 | 45% helix, 17% strand | Q05514 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.87 | 0.93 | 49 | EDO |
| 2 | 1076 | 0.78 | 0.80 | 94 | empty |
| 3 | 133 | 0.47 | 0.78 | 23 | empty |
| 4 | 103 | 0.40 | 0.76 | 21 | empty |
| 5 | 52 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2503 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 1KD0 · Crystal Structure of beta-methylaspartase from Clostridium tetanomorphum. Apo-structure. · 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 1KD0 · PDBe 1KD0 · UniProt Q05514
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