MolNFT v1 · #105900 · protein
The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745
4RIT: “The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.66). MolNFT v1 #105900 on GenesisL1: 3D structure…
- PDB
- 4RIT
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal-dependent decarboxylase
- EC
- 4.1.1.15
- UniProt
- D1C7D8
- Ligands
- CL
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 469 | 45% helix, 13% strand | D1C7D8 |
| A | Pyridoxal-dependent decarboxylase (EC 4.1.1.15) | protein | 461 | 45% helix, 13% strand | D1C7D8 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, A
- GOL · Glycerol · additive · 11 copies · chains B, A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.66 | 0.78 | 48 | empty |
| 2 | 440 | 0.65 | 0.78 | 44 | empty |
| 3 | 66 | 0.45 | 0.82 | 15 | GOL |
| 4 | 83 | 0.44 | 0.80 | 19 | empty |
| 5 | 158 | 0.44 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- B–A · 6698 Ų buried · 85 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered, cofactor).
Compared structures
- 4RIT · The yellow crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter… · 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 4RIT · PDBe 4RIT · UniProt D1C7D8
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