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The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
Analyse The clear crystal structure of 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
- 4RLG
- Type
- protein
- Length
- 1,881 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, ABU, K
- Pockets
- 14 · best druggability 0.67
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 | 472 | 44% helix, 13% strand | D1C7D8 |
| B | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 470 | 45% helix, 13% strand | D1C7D8 |
| D | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 470 | 45% helix, 13% strand | D1C7D8 |
| C | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 469 | 45% helix, 13% strand | D1C7D8 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, D, C
- ABU · Gamma-amino-butanoic acid · ligand · 2 copies · chains D, C
- K · Potassium ion · metal · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.67 | 0.78 | 49 | GOL |
| 2 | 317 | 0.65 | 0.81 | 46 | ABU |
| 3 | 282 | 0.63 | 0.80 | 40 | empty |
| 4 | 347 | 0.62 | 0.78 | 40 | empty |
| 5 | 342 | 0.55 | 0.74 | 35 | empty |
Interfaces
4 interfaces between chains.
- D–C · 7593 Ų buried · 102 hydrogen bonds · protein-protein
- A–B · 7303 Ų buried · 96 hydrogen bonds · protein-protein
- B–D · 123 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 modified, 4 covalent (engineered, covalent ligand, cofactor).
Compared structures
- 4RLG · The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter… · 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 4RLG · PDBe 4RLG · UniProt D1C7D8
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