Research workbench
Human Fab 1E6 bound to fhbp variant 3 from neisseria meningitidis serogroup B
Analyse Human Fab 1E6 bound to fhbp variant 3 from neisseria meningitidis serogroup B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H2Y
- Type
- protein
- Length
- 662 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein GNA1870; Heavy chain; Light chain
- UniProt
- Q19KF7
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Lipoprotein GNA1870 | protein | 231 | 1% helix, 57% strand | Q19KF7 |
| H | Heavy chain | protein | 219 | 6% helix, 48% strand | — |
| L | Light chain | protein | 212 | 8% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 12 copies · chains H, L
- PEG · Di(hydroxyethyl)ether · additive · chains H
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains H, L
- PG4 · Tetraethylene glycol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.74 | 0.93 | 32 | empty |
| 2 | 415 | 0.67 | 0.79 | 42 | empty |
| 3 | 190 | 0.56 | 0.80 | 35 | empty |
| 4 | 311 | 0.51 | 0.73 | 41 | EDO, PEG, P33 |
| 5 | 85 | 0.48 | 0.82 | 22 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1902 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 608 Ų buried · 3 hydrogen bonds · protein-protein
- D–L · 544 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6H2Y · human Fab 1E6 bound to fHbp variant 3 from Neisseria meningitidis serogroup B · 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 Q19KF7
- Elsewhere: RCSB PDB 6H2Y · PDBe 6H2Y · UniProt Q19KF7
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