Research workbench
Crystal structure of the cedar henipavirus attachment G glycoprotein globular domain in complex with the receptor ephrin-B1
Analyse Crystal structure of the cedar henipavirus attachment G glycoprotein globular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P7S
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein; Ephrin-B1
- UniProt
- J7H333, P52795
- Ligands
- NAG, BMA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Attachment glycoprotein | protein | 415 | 3% helix, 46% strand | J7H333 |
| B | Ephrin-B1 | protein | 139 | 7% helix, 32% strand | P52795 |
| D | Ephrin-B1 | protein | 138 | 7% helix, 27% strand | P52795 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.83 | 0.84 | 75 | empty |
| 2 | 875 | 0.82 | 0.84 | 63 | empty |
| 3 | 264 | 0.76 | 0.89 | 52 | empty |
| 4 | 177 | 0.67 | 0.86 | 37 | empty |
| 5 | 275 | 0.55 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1539 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1520 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 257 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6P7S · 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
- P52795 · AlphaFold monomer V2.0 prediction for ephrin-B1 (P52795) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P52795
- Elsewhere: RCSB PDB 6P7S · PDBe 6P7S · UniProt J7H333 · UniProt P52795
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