MolNFT v1 · #105906 · protein
The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
4RIZ: “The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm…”. X-ray diffraction, 2 ligands (PMP, NA), 13 pockets (best druggability 0.76). MolNFT v1 #105906 on GenesisL1: 3D…
- PDB
- 4RIZ
- Type
- protein
- Length
- 1,893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal-dependent decarboxylase
- EC
- 4.1.1.15
- UniProt
- D1C7D8
- Ligands
- PMP, NA
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 470 | 46% helix, 13% strand | D1C7D8 |
| B | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 475 | 45% helix, 13% strand | D1C7D8 |
| C | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 476 | 43% helix, 13% strand | D1C7D8 |
| D | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 472 | 45% helix, 13% strand | D1C7D8 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.76 | 0.79 | 85 | empty |
| 2 | 777 | 0.75 | 0.80 | 60 | empty |
| 3 | 803 | 0.75 | 0.79 | 70 | empty |
| 4 | 759 | 0.75 | 0.80 | 64 | empty |
| 5 | 135 | 0.52 | 0.80 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 6989 Ų buried · 98 hydrogen bonds · protein-protein
- C–D · 6885 Ų buried · 91 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 3 covalent (cofactor, covalent ligand).
Compared structures
- 4RIZ · The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from… · the same entry in another collection · 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 D1C7D8
- Elsewhere: RCSB PDB 4RIZ · PDBe 4RIZ · UniProt D1C7D8
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