Research workbench
Nipah virus attachment glycoprotein in complex with human cell surface receptor EPHRINB2
Analyse Nipah virus attachment glycoprotein in complex with human cell surface receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSM
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase; Ephrin-B2
- EC
- 3.2.1.18
- UniProt
- Q9IH62, P52799
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 413 | 4% helix, 48% strand | Q9IH62 |
| B | Ephrin-B2 | protein | 137 | 10% helix, 33% strand | P52799 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.81 | 0.89 | 43 | empty |
| 2 | 527 | 0.71 | 0.80 | 69 | empty |
| 3 | 143 | 0.49 | 0.78 | 30 | empty |
| 4 | 112 | 0.41 | 0.76 | 21 | empty |
| 5 | 112 | 0.40 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1495 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2VSM · Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2 · 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 0.96
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 Q9IH62
- Every structure of UniProt P52799
- Elsewhere: RCSB PDB 2VSM · PDBe 2VSM · UniProt Q9IH62 · UniProt P52799
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