Research workbench
Ghanaian henipavirus (Gh-M74a) attachment glycoprotein in complex with human ephrinB2
Analyse Ghanaian henipavirus (Gh-M74a) attachment glycoprotein in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UF7
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- BAT PARAMYXOVIRUS EID_HEL/GH-M74A/GHA/2009; Homo sapiens
- Molecule
- Glycoprotein; Ephrin-B2
- UniProt
- I0E093, P52799
- Ligands
- NAG, SO4, CL
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.7 · 4 distinct chains · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein | protein | 417 | 6% helix, 47% strand | I0E093 |
| B | Glycoprotein | protein | 412 | 6% helix, 47% strand | I0E093 |
| C | Ephrin-B2 | protein | 138 | 9% helix, 36% strand | P52799 |
| E | Ephrin-B2 | protein | 139 | 9% helix, 37% strand | P52799 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, E, B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 7 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.82 | 0.84 | 78 | SO4 |
| 2 | 721 | 0.79 | 0.84 | 48 | SO4 |
| 3 | 773 | 0.71 | 0.77 | 72 | empty |
| 4 | 360 | 0.58 | 0.76 | 41 | empty |
| 5 | 189 | 0.56 | 0.80 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1284 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1260 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 99 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4UF7 · Ghanaian henipavirus (gh-M74A) attachment glycoprotein in complex with human 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 E 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 I0E093
- Every structure of UniProt P52799
- Elsewhere: RCSB PDB 4UF7 · PDBe 4UF7 · UniProt I0E093 · UniProt P52799
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