Research workbench
Cedar virus attachment glycoprotein (G) in complex with human ephrin- B1
Analyse Cedar virus attachment glycoprotein (G) in complex with human ephrin- B1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6THG
- Type
- protein
- Length
- 2,763 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Attachment glycoprotein; Ephrin-B1
- UniProt
- A0A185KRV2, P98172
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Attachment glycoprotein | protein | 419 | 6% helix, 46% strand | A0A185KRV2 |
| D, C, J | Ephrin-B1 | protein | 136 | 10% helix, 22% strand | P98172 |
| A | Attachment glycoprotein | protein | 418 | 6% helix, 45% strand | A0A185KRV2 |
| E, G | Attachment glycoprotein | protein | 415 | 6% helix, 46% strand | A0A185KRV2 |
| I | Attachment glycoprotein | protein | 417 | 6% helix, 47% strand | A0A185KRV2 |
| F | Ephrin-B1 | protein | 137 | 9% helix, 22% strand | P98172 |
| H | Ephrin-B1 | protein | 134 | 10% helix, 23% strand | P98172 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 copies · chains B, C, A, D, E, H, F, I, G, J
- BMA · beta-D-mannopyranose · sugar · 6 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.86 | 0.90 | 78 | empty |
| 2 | 497 | 0.84 | 0.90 | 46 | empty |
| 3 | 763 | 0.83 | 0.86 | 72 | empty |
| 4 | 753 | 0.82 | 0.85 | 75 | empty |
| 5 | 711 | 0.81 | 0.85 | 64 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1563 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1558 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1538 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1534 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1257 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
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 A0A185KRV2
- Every structure of UniProt P98172
- Elsewhere: RCSB PDB 6THG · PDBe 6THG · UniProt A0A185KRV2 · UniProt P98172
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