Research workbench
Crystal structure of treponema pallidum TP0751 (pallilysin)
Analyse Crystal structure of treponema pallidum TP0751 (pallilysin) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JK2
- Type
- protein
- Length
- 1,106 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TP0751
- UniProt
- O83732
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 9 distinct chains · 14% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TP0751 | protein | 128 | 13% helix, 48% strand | O83732 |
| B | TP0751 | protein | 125 | 14% helix, 52% strand | O83732 |
| C | TP0751 | protein | 122 | 16% helix, 52% strand | O83732 |
| D | TP0751 | protein | 128 | 14% helix, 51% strand | O83732 |
| E | TP0751 | protein | 128 | 14% helix, 51% strand | O83732 |
| F | TP0751 | protein | 123 | 15% helix, 53% strand | O83732 |
| G | TP0751 | protein | 117 | 14% helix, 50% strand | O83732 |
| H | TP0751 | protein | 119 | 14% helix, 52% strand | O83732 |
| I | TP0751 | protein | 116 | 16% helix, 54% strand | O83732 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.67 | 0.79 | 63 | empty |
| 2 | 233 | 0.61 | 0.81 | 46 | empty |
| 3 | 206 | 0.60 | 0.81 | 36 | empty |
| 4 | 141 | 0.52 | 0.80 | 30 | empty |
| 5 | 64 | 0.48 | 0.84 | 12 | empty |
Interfaces
8 interfaces between chains.
- E–I · 835 Ų buried · 5 hydrogen bonds · protein-protein
- F–H · 807 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 797 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 486 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 465 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JK2 · Crystal structure of Treponema pallidum Tp0751 (Pallilysin) · the same entry in another collection · chain I against I, TM-score 1.00
- O83732 · AlphaFold monomer V2.0 prediction for uncharacterized protein TP_0751 (O83732) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 O83732
- Elsewhere: RCSB PDB 5JK2 · PDBe 5JK2 · UniProt O83732
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