Research workbench
Crystal structure of human endogenous retrovirus herv-frd envelope protein (syncitin-2)
Analyse Crystal structure of human endogenous retrovirus herv-frd envelope protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y4M
- Type
- protein
- Length
- 159 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Herv-FRD_6P24.1 provirus ancestral env polyprotein
- UniProt
- P60508
- Ligands
- CL
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Herv-FRD_6P24.1 provirus ancestral env polyprotein | protein | 53 | 68% helix, 0% strand | P60508 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 974 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 970 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 941 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1Y4M · Crystal structure of human endogenous retrovirus HERV-FRD envelope protein (syncitin-2) · the same entry in another collection · chain A against A, TM-score 1.00
- P60508 · AlphaFold monomer V2.0 prediction for syncytin-2 (P60508) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P60508
- Elsewhere: RCSB PDB 1Y4M · PDBe 1Y4M · UniProt P60508
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