MolNFT v1 · #101871 · protein
Crystal structure of the vaccine antigen transferrin binding protein B (tbpb) mutant TRP-176-ala from haemophilus parasuis HP5
4O4U: “Crystal structure of the vaccine antigen transferrin binding protein B (tbpb) mutant TRP-176-ala from…”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #101871 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4O4U
- Type
- protein
- Length
- 2,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tbpb
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tbpb | protein | 505 | 3% helix, 50% strand | — |
| B | Tbpb | protein | 500 | 3% helix, 50% strand | — |
| C | Tbpb | protein | 499 | 3% helix, 48% strand | — |
| D | Tbpb | protein | 507 | 3% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.78 | 0.82 | 119 | empty |
| 2 | 781 | 0.78 | 0.82 | 97 | empty |
| 3 | 803 | 0.69 | 0.76 | 79 | empty |
| 4 | 204 | 0.66 | 0.85 | 32 | empty |
| 5 | 319 | 0.66 | 0.81 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–D · 541 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 445 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 409 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4O4U · Crystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant… · 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 4O4U · PDBe 4O4U
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