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The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Analyse The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RM1
- 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, CL
- Pockets
- 12 · best druggability 0.77
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 | 473 | 45% helix, 13% strand | D1C7D8 |
| A | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 474 | 45% helix, 14% strand | D1C7D8 |
| C | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 476 | 45% helix, 13% strand | D1C7D8 |
| D | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 470 | 44% helix, 13% strand | D1C7D8 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 2 copies · chains B, A, C, D
- CL · Chloride ion · ion · 2 copies · chains B, A, C, D
- GOL · Glycerol · additive · 6 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.77 | 0.79 | 85 | empty |
| 2 | 989 | 0.76 | 0.79 | 80 | empty |
| 3 | 782 | 0.75 | 0.80 | 58 | GOL |
| 4 | 729 | 0.74 | 0.80 | 62 | GOL |
| 5 | 1074 | 0.72 | 0.76 | 112 | empty |
Interfaces
6 interfaces between chains.
- B–A · 6978 Ų buried · 83 hydrogen bonds · protein-protein
- C–D · 6901 Ų buried · 103 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (cofactor, covalent ligand).
Compared structures
- 4RM1 · The crystal structure of Y333Q 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 4RM1 · PDBe 4RM1 · UniProt D1C7D8
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