Research workbench
Inferred receptor binding domain of human endogenous retrovirus envelope ENVP(B)1
Analyse Inferred receptor binding domain of human endogenous retrovirus envelope… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W5Y
- Type
- protein
- Length
- 479 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENVP(B)1 inferred receptor binding domain
- Ligands
- NAG, BMA, FUC
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENVP(B)1 inferred receptor binding domain | protein | 154 | 16% helix, 29% strand | — |
| B | ENVP(B)1 inferred receptor binding domain | protein | 163 | 12% helix, 27% strand | — |
| C | ENVP(B)1 inferred receptor binding domain | protein | 162 | 12% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.60 | 0.78 | 37 | GOL |
Interfaces
2 interfaces between chains.
- B–C · 855 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6W5Y · Inferred receptor binding domain of human endogenous retrovirus envelope EnvP(b)1 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6W5Y · PDBe 6W5Y
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