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Crystal structure of hendra receptor binding protein head domain in complex with human neutralizing antibody henv-32
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
- 6VY4
- Type
- protein
- Length
- 1,674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor binding protein; Anti-hendra receptor binding protein antibody henv-32 Fab heavy…
- UniProt
- F4YH71
- Ligands
- NAG, SO4
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor binding protein | protein | 422 | 8% helix, 47% strand | F4YH71 |
| B | Receptor binding protein | protein | 426 | 5% helix, 47% strand | F4YH71 |
| C | Anti-hendra receptor binding protein antibody henv-32 Fab heavy chain | protein | 207 | 4% helix, 50% strand | — |
| D | Anti-hendra receptor binding protein antibody henv-32 Fab light chain | protein | 198 | 8% helix, 47% strand | — |
| H | Anti-hendra receptor binding protein antibody henv-32 Fab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| L | Anti-hendra receptor binding protein antibody henv-32 Fab light chain | protein | 210 | 8% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, H
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, H, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.85 | 0.87 | 97 | IPA |
| 2 | 268 | 0.69 | 0.85 | 32 | empty |
| 3 | 410 | 0.66 | 0.79 | 40 | empty |
| 4 | 129 | 0.65 | 0.88 | 21 | empty |
| 5 | 295 | 0.62 | 0.79 | 35 | empty |
Interfaces
12 interfaces between chains.
- H–L · 1622 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1614 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 909 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 805 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 725 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6VY4 · 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 6VY4 · PDBe 6VY4 · UniProt F4YH71
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