MolNFT v1 · #139182 · protein
Crystal structure of meso-diaminopimelate decarboxylase (dapdc) from corynebacterium glutamicum
5X7M: “Crystal structure of meso-diaminopimelate decarboxylase (dapdc) from corynebacterium glutamicum”. X-ray diffraction, 1 ligand (PLP), 10 pockets (best druggability 0.77). MolNFT v1 #139182 on GenesisL1: 3D structure, binding sites…
- PDB
- 5X7M
- Type
- protein
- Length
- 886 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
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diaminopimelate decarboxylase (EC 4.1.1.20) | protein | 443 | 34% helix, 27% strand | P09890 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.77 | 0.98 | 21 | empty |
| 2 | 84 | 0.76 | 0.98 | 22 | empty |
| 3 | 500 | 0.72 | 0.81 | 73 | PLP |
| 4 | 454 | 0.71 | 0.81 | 56 | PLP |
| 5 | 425 | 0.66 | 0.79 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 3403 Ų buried · 64 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5X7M · 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 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 P09890
- Elsewhere: RCSB PDB 5X7M · PDBe 5X7M · UniProt P09890
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