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Crystal structure of the vaccine antigen transferrin binding protein B (tbpb) double mutant tyr-167-ala and TRP-176-ala from haemophilus parasuis HP5
Analyse Crystal structure of the vaccine antigen transferrin binding protein B (tbpb)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O4X
- Type
- protein
- Length
- 1,005 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tbpb
- Ligands
- NA, SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tbpb | protein | 503 | 3% helix, 51% strand | — |
| B | Tbpb | protein | 502 | 5% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 9 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.73 | 0.78 | 81 | GOL |
| 2 | 681 | 0.70 | 0.78 | 61 | empty |
| 3 | 160 | 0.48 | 0.77 | 34 | empty |
| 4 | 181 | 0.46 | 0.75 | 22 | empty |
| 5 | 79 | 0.43 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4O4X · Crystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) double… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 4O4X · PDBe 4O4X
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