MolNFT v1 · #9093 · protein
Mycobacterium diaminopimelate dicarboxylase (lysa)
1HKW · Diaminopimelate decarboxylase: “Mycobacterium diaminopimelate dicarboxylase (lysa)”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.74). MolNFT v1 #9093 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1HKW
- Type
- protein
- Length
- 890 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
- SO4
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 446 | 31% helix, 28% strand | P31848 |
| B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 444 | 31% helix, 28% strand | P31848 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.74 | 0.98 | 21 | empty |
| 2 | 70 | 0.73 | 0.98 | 21 | empty |
| 3 | 422 | 0.68 | 0.80 | 61 | SO4 |
| 4 | 395 | 0.65 | 0.79 | 55 | SO4 |
| 5 | 128 | 0.57 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3561 Ų buried · 80 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 1HKW · 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 1HKW · PDBe 1HKW · UniProt P31848
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