MolNFT v1 · #9092 · protein
Mycobacterium diaminopimelate dicarboxylase (lysa)
1HKV · Diaminopimelate decarboxylase: “Mycobacterium diaminopimelate dicarboxylase (lysa)”. X-ray diffraction, 2 ligands (LYS, PLP), 11 pockets (best druggability 0.74). MolNFT v1 #9092 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1HKV
- Type
- protein
- Length
- 892 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- P31848
- Ligands
- LYS, PLP
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 446 | 33% helix, 27% strand | P31848 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 23 | empty |
| 2 | 59 | 0.72 | 0.98 | 19 | empty |
| 3 | 493 | 0.72 | 0.82 | 62 | LYS, PLP |
| 4 | 455 | 0.70 | 0.81 | 64 | LYS, PLP |
| 5 | 124 | 0.58 | 0.84 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3670 Ų buried · 81 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 1HKV · mycobacterium diaminopimelate dicarboxylase (lysa) · 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 P31848
- Elsewhere: RCSB PDB 1HKV · PDBe 1HKV · UniProt P31848
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