Research workbench
Crystal structure of cystalysin from treponema denticola contains a pyridoxal 5'-phosphate-L-aminoethoxyvinylglycine complex
Analyse Crystal structure of cystalysin from treponema denticola contains a pyridoxal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C7O
- Type
- protein
- Length
- 3,152 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cystalysin
- UniProt
- Q56257
- Ligands
- PPG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Cystalysin | protein | 394 | 46% helix, 15% strand | Q56257 |
Ligands and binding sites
- PPG · (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.84 | 0.86 | 117 | PPG |
| 2 | 927 | 0.83 | 0.84 | 131 | PPG |
| 3 | 764 | 0.83 | 0.86 | 96 | PPG |
| 4 | 936 | 0.83 | 0.84 | 123 | PPG |
| 5 | 429 | 0.61 | 0.76 | 46 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1999 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1998 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1983 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1966 Ų buried · 25 hydrogen bonds · protein-protein
- D–G · 287 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1C7O · Crystal structure of cystalysin from treponema denticola contains a pyridoxal… · 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 Q56257
- Elsewhere: RCSB PDB 1C7O · PDBe 1C7O · UniProt Q56257
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