Research workbench
Crystal structure of antigen TPF1 from treponema pallidum
Analyse Crystal structure of antigen TPF1 from treponema pallidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FJC
- Type
- protein
- Length
- 2,416 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen TPF1
- UniProt
- P16665
- Ligands
- FE
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, H, I, J, K, L, M, P | Antigen TPF1 | protein | 151 | 79% helix, 3% strand | P16665 |
| B | Antigen TPF1 | protein | 156 | 77% helix, 4% strand | P16665 |
| C, E, G, N, O | Antigen TPF1 | protein | 150 | 80% helix, 3% strand | P16665 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 16 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.74 | 0.82 | 91 | empty |
| 2 | 439 | 0.72 | 0.82 | 81 | empty |
| 3 | 633 | 0.71 | 0.78 | 108 | empty |
| 4 | 301 | 0.66 | 0.82 | 34 | empty |
| 5 | 306 | 0.65 | 0.81 | 38 | empty |
Interfaces
35 interfaces between chains.
- F–G · 1311 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1310 Ų buried · 21 hydrogen bonds · protein-protein
- M–N · 1306 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1304 Ų buried · 22 hydrogen bonds · protein-protein
- E–H · 1300 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2FJC · Crystal structure of antigen TpF1 from Treponema pallidum · the same entry in another collection · chain P against P, 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 P16665
- Elsewhere: RCSB PDB 2FJC · PDBe 2FJC · UniProt P16665
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