MolNFT v1 · #16710 · protein
TP47, the 47-kilodalton lipoprotein of treponema pallidum
1O75 · 47 kda membrane antigen: “TP47, the 47-kilodalton lipoprotein of treponema pallidum”. X-ray diffraction, 2 ligands (PDX, XE), 11 pockets (best druggability 0.78). MolNFT v1 #16710 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1O75
- Type
- protein
- Length
- 801 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 47 kda membrane antigen
- UniProt
- P29723
- Ligands
- PDX, XE
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 47 kda membrane antigen | protein | 399 | 10% helix, 49% strand | P29723 |
| B | 47 kda membrane antigen | protein | 402 | 10% helix, 47% strand | P29723 |
Ligands and binding sites
- PDX · 2,3-di-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- XE · Xenon · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.78 | 0.80 | 125 | empty |
| 2 | 372 | 0.66 | 0.80 | 54 | empty |
| 3 | 290 | 0.65 | 0.81 | 39 | PDX |
| 4 | 319 | 0.54 | 0.75 | 55 | empty |
| 5 | 297 | 0.52 | 0.74 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 2028 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1O75 · Tp47, the 47-Kilodalton Lipoprotein of Treponema pallidum · the same entry in another collection · chain A against A, TM-score 1.00
- P29723 · AlphaFold monomer V2.0 prediction for putative dd-carboxypeptidase TP_0574 (P29723) · a predicted model of the same protein · chain B 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 P29723
- Elsewhere: RCSB PDB 1O75 · PDBe 1O75 · UniProt P29723
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