MolNFT v1 · #28130 · protein

Crystal structure of human endogenous retrovirus herv-frd envelope protein (syncitin-2)

1Y4M · Herv-FRD_6P24.1 provirus ancestral env polyprotein: “Crystal structure of human endogenous retrovirus herv-frd envelope protein (syncitin-2)”. X-ray diffraction, 1 ligand (CL). MolNFT v1 #28130 on GenesisL1: 3D structure, binding…

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 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 970 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 941 Å² 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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