MolNFT v1 · #170201 · protein
Crystal structure of the meningococcal vaccine antigen fhbp in complex with a cross-reactive human Fab.
6XZW · LIPOPROT_C domain-containing protein: “Crystal structure of the meningococcal vaccine antigen fhbp in complex with a cross-reactive human Fab.”. X-ray diffraction, 8 pockets (best druggability 0.56). MolNFT v1 #170201 on GenesisL1…
- PDB
- 6XZW
- Type
- protein
- Length
- 669 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIPOPROT_C domain-containing protein; Fab 4B3 (light chain); Fab 4B3 (heavy chain)
- UniProt
- Q9JXV4
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | LIPOPROT_C domain-containing protein | protein | 239 | 6% helix, 59% strand | Q9JXV4 |
| L | Fab 4B3 (light chain) | protein | 214 | 7% helix, 50% strand | — |
| H | Fab 4B3 (heavy chain) | protein | 216 | 7% helix, 49% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains D, L, H
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 | 338 | 0.56 | 0.76 | 46 | empty |
| 2 | 61 | 0.54 | 0.88 | 19 | empty |
| 3 | 186 | 0.49 | 0.77 | 31 | empty |
| 4 | 71 | 0.46 | 0.82 | 21 | empty |
| 5 | 132 | 0.42 | 0.76 | 25 | EDO |
Interfaces
3 interfaces between chains.
- L–H · 1671 Ų buried · 17 hydrogen bonds · protein-protein
- D–H · 507 Ų buried · 9 hydrogen bonds · protein-protein
- D–L · 454 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6XZW · Crystal structure of the meningococcal vaccine antigen fHbp in complex with a… · the same entry in another collection · chain D against D, 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 Q9JXV4
- Elsewhere: RCSB PDB 6XZW · PDBe 6XZW · UniProt Q9JXV4
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