MolNFT v1 · #105907 · protein
The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
4RJ0: “The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm…”. X-ray diffraction, 2 ligands (PMP, PO4), 16 pockets (best druggability 0.75). MolNFT v1 #105907 on GenesisL1: 3D…
- PDB
- 4RJ0
- Type
- protein
- Length
- 1,869 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, PO4
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 471 | 45% helix, 13% strand | D1C7D8 |
| A | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 467 | 44% helix, 13% strand | D1C7D8 |
| C | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 463 | 47% helix, 13% strand | D1C7D8 |
| D | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 468 | 45% helix, 13% strand | D1C7D8 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains C, D
- PO4 · Phosphate ion · ion · chains C
- GOL · Glycerol · additive · 3 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.75 | 0.80 | 65 | empty |
| 2 | 655 | 0.73 | 0.80 | 57 | empty |
| 3 | 914 | 0.72 | 0.76 | 95 | empty |
| 4 | 554 | 0.70 | 0.79 | 44 | empty |
| 5 | 422 | 0.66 | 0.79 | 45 | empty |
Interfaces
6 interfaces between chains.
- C–D · 6790 Ų buried · 97 hydrogen bonds · protein-protein
- B–A · 6783 Ų buried · 109 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 68 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (cofactor, covalent ligand).
Compared structures
- 4RJ0 · The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from… · the same entry in another collection · chain B against B, 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 4RJ0 · PDBe 4RJ0 · UniProt D1C7D8
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