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Crystal structure of the isotype 1 transferrin binding protein B (tbpb) from serogroup B neisseria meningitidis
Analyse Crystal structure of the isotype 1 transferrin binding protein B (tbpb) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QQ1
- Type
- protein
- Length
- 1,521 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin-binding protein 2
- UniProt
- Q06988
- Ligands
- CS, SO4
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin-binding protein 2 | protein | 521 | 5% helix, 44% strand | Q06988 |
| B | Transferrin-binding protein 2 | protein | 485 | 4% helix, 46% strand | Q06988 |
| C | Transferrin-binding protein 2 | protein | 515 | 4% helix, 44% strand | Q06988 |
Ligands and binding sites
- CS · Cesium ion · metal · 8 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.68 | 0.78 | 61 | empty |
| 2 | 485 | 0.67 | 0.79 | 48 | empty |
| 3 | 129 | 0.55 | 0.83 | 19 | empty |
| 4 | 190 | 0.53 | 0.78 | 28 | empty |
| 5 | 190 | 0.50 | 0.77 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 475 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 193 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4QQ1 · Crystal structure of the isotype 1 Transferrin binding protein B (TbpB) from serogroup B… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06988 · AlphaFold monomer V2.0 prediction for transferrin-binding protein B (Q06988) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q06988
- Elsewhere: RCSB PDB 4QQ1 · PDBe 4QQ1 · UniProt Q06988
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