Research workbench
Meso-diaminopimelate decarboxylase from arabidopsis thaliana (isoform 1)
Analyse Meso-diaminopimelate decarboxylase from arabidopsis thaliana (isoform 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N2A
- Type
- protein
- Length
- 833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase 1, chloroplastic
- EC
- 4.1.1.20
- UniProt
- Q949X7
- Ligands
- PLP, LYS
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase 1, chloroplastic (EC 4.1.1.20) | protein | 422 | 35% helix, 25% strand | Q949X7 |
| B | Diaminopimelate decarboxylase 1, chloroplastic (EC 4.1.1.20) | protein | 411 | 33% helix, 26% strand | Q949X7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.67 | 0.82 | 38 | empty |
| 2 | 300 | 0.67 | 0.82 | 55 | PLP, LYS |
| 3 | 428 | 0.66 | 0.79 | 60 | PLP, LYS |
| 4 | 320 | 0.64 | 0.80 | 39 | empty |
| 5 | 289 | 0.58 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3615 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 6N2A · Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 1) · the same entry in another collection · chain A against A, TM-score 1.00
- Q949X7 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase 1, chloroplastic… · a predicted model of the same protein · 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 Q949X7
- Elsewhere: RCSB PDB 6N2A · PDBe 6N2A · UniProt Q949X7
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