MolNFT v1 · #29290 · protein
The crystal structure of a dgd mutant: Q52A
1Z3Z · Dialkylglycine decarboxylase: “The crystal structure of a dgd mutant: Q52A”. X-ray diffraction, 3 ligands (PLP, NA, K), 3 pockets (best druggability 0.56). MolNFT v1 #29290 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1Z3Z
- Type
- protein
- Length
- 431 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dialkylglycine decarboxylase
- EC
- 4.1.1.64
- UniProt
- P16932
- Ligands
- PLP, NA, K
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dialkylglycine decarboxylase (EC 4.1.1.64) | protein | 431 | 39% helix, 18% strand | P16932 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- K · Potassium ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.56 | 0.75 | 61 | PLP, MES |
| 2 | 224 | 0.52 | 0.76 | 27 | empty |
| 3 | 88 | 0.40 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 P16932
- Elsewhere: RCSB PDB 1Z3Z · PDBe 1Z3Z · UniProt P16932
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