Research workbench
Crystal structure of a D,L-lysine complex of diaminopimelate decarboxylase
Analyse Crystal structure of a D,L-lysine complex of diaminopimelate decarboxylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KO0
- Type
- protein
- Length
- 419 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- P00861
- Ligands
- PLP, LYS, DLY
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 419 | 31% helix, 23% strand | P00861 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- LYS · Lysine · ligand · chains A
- DLY · D-lysine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.62 | 0.75 | 48 | PLP, LYS, DLY |
| 2 | 81 | 0.33 | 0.74 | 19 | empty |
| 3 | 57 | 0.29 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1KO0 · Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase · the same entry in another collection · chain A against A, TM-score 1.00
- P00861 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (P00861) · a predicted model of the same protein · chain A 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 P00861
- Elsewhere: RCSB PDB 1KO0 · PDBe 1KO0 · UniProt P00861
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