MolNFT v1 · #55613 · protein
Crystal structure of the meningococcal vaccine antigen factor H binding protein in complex with a bactericidal antibody
2YPV · Lipoprotein: “Crystal structure of the meningococcal vaccine antigen factor H binding protein in complex with a…”. X-ray diffraction, 8 pockets (best druggability 0.71). MolNFT v1 #55613 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YPV
- Type
- protein
- Length
- 656 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein; Fab 12C1
- UniProt
- Q6QCC2
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipoprotein | protein | 229 | 7% helix, 60% strand | Q6QCC2 |
| H | Fab 12C1 | protein | 215 | 7% helix, 51% strand | — |
| L | Fab 12C1 | protein | 212 | 6% helix, 51% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.71 | 0.78 | 75 | EDO |
| 2 | 74 | 0.52 | 0.85 | 20 | empty |
| 3 | 175 | 0.48 | 0.77 | 30 | EDO |
| 4 | 60 | 0.40 | 0.80 | 13 | empty |
| 5 | 85 | 0.35 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1905 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 624 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 507 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2YPV · Crystal structure of the Meningococcal vaccine antigen factor H binding protein in… · 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
- Every structure of UniProt Q6QCC2
- Elsewhere: RCSB PDB 2YPV · PDBe 2YPV · UniProt Q6QCC2
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