MolNFT v1 · #139183 · protein
Crystal structure of meso-diaminopimelate decarboxylase (dapdc) from corynebacterium glutamicum
5X7N: “Crystal structure of meso-diaminopimelate decarboxylase (dapdc) from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (PLP, LYS), 11 pockets (best druggability 0.77). MolNFT v1 #139183 on GenesisL1: 3D structure, binding…
- PDB
- 5X7N
- Type
- protein
- Length
- 881 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diaminopimelate decarboxylase
- EC
- 4.1.1.20
- UniProt
- P09890
- Ligands
- PLP, LYS
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 442 | 34% helix, 27% strand | P09890 |
| B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 439 | 33% helix, 28% strand | P09890 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- LYS · Lysine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.77 | 0.98 | 24 | GOL |
| 2 | 57 | 0.73 | 0.99 | 20 | GOL |
| 3 | 481 | 0.71 | 0.81 | 63 | PLP, LYS |
| 4 | 63 | 0.68 | 0.95 | 19 | PLP |
| 5 | 405 | 0.65 | 0.79 | 45 | PLP, LYS |
Interfaces
1 interface between chains.
- A–B · 3239 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5X7N · Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- P09890 · AlphaFold monomer V2.0 prediction for diaminopimelate decarboxylase (P09890) · a predicted model of the same protein · chain B 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 P09890
- Elsewhere: RCSB PDB 5X7N · PDBe 5X7N · UniProt P09890
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