Research workbench
Major tropism determinant P1 (mtd-P1) variant complexed with bordetella brochiseptica virulence factor pertactin extracellular domain (prn-E).
Analyse Major tropism determinant P1 (mtd-P1) variant complexed with bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IOU
- Type
- protein
- Length
- 3,272 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major tropism determinant P1; Pertactin extracellular domain
- UniProt
- Q775D6, Q03035
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Major tropism determinant P1 | protein | 376 | 12% helix, 30% strand | Q775D6 |
| G, H | Pertactin extracellular domain | protein | 508 | 1% helix, 55% strand | Q03035 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.86 | 0.90 | 76 | MG |
| 2 | 635 | 0.86 | 0.91 | 74 | MG |
| 3 | 378 | 0.81 | 0.90 | 46 | empty |
| 4 | 342 | 0.80 | 0.90 | 38 | empty |
| 5 | 894 | 0.79 | 0.81 | 94 | empty |
Interfaces
17 interfaces between chains.
- A–C · 2407 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2404 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2397 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 2371 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2367 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2IOU · Major Tropism Determinant P1 (Mtd-P1) Variant Complexed with Bordetella brochiseptica… · the same entry in another collection · chain H against H, TM-score 1.00
- Q03035 · AlphaFold monomer V2.0 prediction for pertactin autotransporter (Q03035) · a predicted model of the same protein · chain G 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 Q775D6
- Every structure of UniProt Q03035
- Elsewhere: RCSB PDB 2IOU · PDBe 2IOU · UniProt Q775D6 · UniProt Q03035
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