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Crystal structure of hendra receptor binding protein head domain in complex with human neutralizing antibody henv-26
Analyse Crystal structure of hendra receptor binding protein head domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VY6
- Type
- protein
- Length
- 853 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor binding protein; Anti-hendra receptor binding protein antibody henv-26 Fab heavy…
- UniProt
- F4YH71
- Ligands
- NAG, ZN, SO4, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor binding protein | protein | 415 | 4% helix, 48% strand | F4YH71 |
| H | Anti-hendra receptor binding protein antibody henv-26 Fab heavy chain | protein | 226 | 6% helix, 49% strand | — |
| L | Anti-hendra receptor binding protein antibody henv-26 Fab light chain | protein | 212 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, L
- ZN · Zinc ion · metal · chains L
- SO4 · Sulfate ion · ion · 5 copies · chains A, H, L
- CL · Chloride ion · ion · chains H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.79 | 0.81 | 76 | empty |
| 2 | 272 | 0.71 | 0.86 | 33 | empty |
| 3 | 145 | 0.53 | 0.80 | 26 | MPD |
| 4 | 225 | 0.51 | 0.76 | 33 | empty |
| 5 | 138 | 0.38 | 0.73 | 36 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1903 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 949 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 487 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6VY6 · Crystal structure of Hendra receptor binding protein head domain in complex with human… · 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 F4YH71
- Elsewhere: RCSB PDB 6VY6 · PDBe 6VY6 · UniProt F4YH71
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