Research workbench
P46, an immunodominant surface protein from mycoplasma hyopneumoniae
Analyse P46, an immunodominant surface protein from mycoplasma hyopneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S3T
- Type
- protein
- Length
- 3,235 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 46 kda surface antigen; Immunoglobulin light chain; Immunoglobulin heavy chain
- UniProt
- P0C0J8
- Ligands
- XYP, NA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 46 kda surface antigen | protein | 374 | 40% helix, 16% strand | P0C0J8 |
| C, I, M, Q | Immunoglobulin light chain | protein | 216 | 7% helix, 47% strand | — |
| D, E, N, R | Immunoglobulin heavy chain | protein | 219 | 4% helix, 48% strand | — |
| S | 46 kda surface antigen | protein | 373 | 39% helix, 17% strand | P0C0J8 |
| T | 46 kda surface antigen | protein | 374 | 39% helix, 17% strand | P0C0J8 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B, S, T
- NA · Sodium ion · metal · 4 copies · chains A, B, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.78 | 0.80 | 145 | empty |
| 2 | 1178 | 0.78 | 0.80 | 160 | empty |
| 3 | 1083 | 0.74 | 0.77 | 90 | empty |
| 4 | 845 | 0.72 | 0.77 | 80 | empty |
| 5 | 796 | 0.69 | 0.76 | 71 | empty |
Interfaces
23 interfaces between chains.
- Q–R · 1872 Ų buried · 15 hydrogen bonds · protein-protein
- M–N · 1856 Ų buried · 13 hydrogen bonds · protein-protein
- I–E · 1814 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1807 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1632 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6S3T · P46, an immunodominant surface protein from Mycoplasma hyopneumoniae · the same entry in another collection · chain Q against Q, 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 P0C0J8
- Elsewhere: RCSB PDB 6S3T · PDBe 6S3T · UniProt P0C0J8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.