MolNFT v1 · #157528 · protein
Meso-diaminopimelate decarboxylase from arabidopsis thaliana (isoform 2)
6N2F · Diaminopimelate decarboxylase 2, chloroplastic: “Meso-diaminopimelate decarboxylase from arabidopsis thaliana (isoform 2)”. X-ray diffraction, 2 ligands (PLP, LYS), 8 pockets (best druggability 0.74). MolNFT v1 #157528 on GenesisL1…
- PDB
- 6N2F
- Type
- protein
- Length
- 834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase 2, chloroplastic
- EC
- 4.1.1.20
- UniProt
- Q94A94
- Ligands
- PLP, LYS
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase 2, chloroplastic (EC 4.1.1.20) | protein | 413 | 32% helix, 28% strand | Q94A94 |
| B | Diaminopimelate decarboxylase 2, chloroplastic (EC 4.1.1.20) | protein | 421 | 32% helix, 26% strand | Q94A94 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.74 | 0.79 | 70 | empty |
| 2 | 198 | 0.69 | 0.87 | 41 | PLP, LYS |
| 3 | 316 | 0.64 | 0.81 | 32 | empty |
| 4 | 299 | 0.64 | 0.81 | 37 | empty |
| 5 | 277 | 0.60 | 0.79 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3355 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 6N2F · Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q94A94 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase 2, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q94A94
- Elsewhere: RCSB PDB 6N2F · PDBe 6N2F · UniProt Q94A94
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