MolNFT v1 · #160008 · protein
Crystal structure of the cedar henipavirus attachment G glycoprotein globular domain in complex with the receptor ephrin-B2
6P7Y · Attachment glycoprotein: “Crystal structure of the cedar henipavirus attachment G glycoprotein globular domain in complex with the…”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 6P7Y
- Type
- protein
- Length
- 1,133 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein; Ephrin-B2
- UniProt
- J7H333, P52799
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Attachment glycoprotein | protein | 430 | 6% helix, 47% strand | J7H333 |
| B | Ephrin-B2 | protein | 137 | 9% helix, 30% strand | P52799 |
| D | Ephrin-B2 | protein | 136 | 7% helix, 31% strand | P52799 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains C, A
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.83 | 0.87 | 58 | empty |
| 2 | 893 | 0.81 | 0.83 | 62 | empty |
| 3 | 323 | 0.71 | 0.84 | 48 | empty |
| 4 | 248 | 0.68 | 0.85 | 46 | empty |
| 5 | 95 | 0.52 | 0.84 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1525 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1496 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 6P7Y · Crystal Structure of the Cedar henipavirus Attachment G Glycoprotein globular domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P52799 · AlphaFold monomer V2.0 prediction for ephrin-B2 (P52799) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 J7H333
- Every structure of UniProt P52799
- Elsewhere: RCSB PDB 6P7Y · PDBe 6P7Y · UniProt J7H333 · UniProt P52799
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