Research workbench
Crystal structure of diaminopimelate decarboxylase from brucella melitensis bound to plp
Analyse Crystal structure of diaminopimelate decarboxylase from brucella melitensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VAB
- Type
- protein
- Length
- 840 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase 1
- EC
- 4.1.1.20
- UniProt
- Q8YJJ9
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diaminopimelate decarboxylase 1 (EC 4.1.1.20) | protein | 420 | 34% helix, 27% strand | Q8YJJ9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.83 | 0.95 | 54 | EDO |
| 2 | 228 | 0.61 | 0.81 | 30 | empty |
| 3 | 229 | 0.60 | 0.80 | 31 | empty |
| 4 | 195 | 0.58 | 0.81 | 37 | empty |
| 5 | 325 | 0.57 | 0.76 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 3875 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 3VAB · Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP · 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 Q8YJJ9
- Elsewhere: RCSB PDB 3VAB · PDBe 3VAB · UniProt Q8YJJ9
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