MolNFT v1 · #81988 · protein
The crystal structure of transferrin binding protein a (tbpa) from neisserial meningitidis serogroup B in complex with full length human transferrin
3V8X · Transferrin-binding protein 1: “The crystal structure of transferrin binding protein a (tbpa) from neisserial meningitidis serogroup B in…”. X-ray diffraction, 5 ligands (NAG, MAN, GAL), 18 pockets (best druggability 0.87). MolNFT…
- PDB
- 3V8X
- Type
- protein
- Length
- 1,529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transferrin-binding protein 1; Serotransferrin
- UniProt
- Q9K0U9, P02787
- Ligands
- NAG, MAN, GAL, BMA, SIA
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transferrin-binding protein 1 | protein | 853 | 8% helix, 54% strand | Q9K0U9 |
| B | Serotransferrin | protein | 676 | 31% helix, 17% strand | P02787 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.87 | 0.93 | 65 | empty |
| 2 | 1124 | 0.85 | 0.86 | 95 | empty |
| 3 | 813 | 0.80 | 0.83 | 90 | empty |
| 4 | 846 | 0.76 | 0.80 | 70 | empty |
| 5 | 745 | 0.74 | 0.79 | 97 | NAG |
Interfaces
1 interface between chains.
- A–B · 2657 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3V8X · The crystal structure of transferrin binding protein A (TbpA) from Neisserial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9K0U9 · AlphaFold monomer V2.0 prediction for transferrin-binding protein a (Q9K0U9) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P02787 · AlphaFold monomer V2.0 prediction for serotransferrin (P02787) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 Q9K0U9
- Every structure of UniProt P02787
- Elsewhere: RCSB PDB 3V8X · PDBe 3V8X · UniProt Q9K0U9 · UniProt P02787
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