KSHV_ORF4
Q2HRD4
The model was generated using Colabfold with 3x recycles
Sequence coverage
pLDDT
Predicted Alignment Error (PAE)
Model rank 1
Model without the signal peptide rank 1
Using DeepTMHMM, this protein was identified to contain a signal peptide and a transmembrane domain.
The transmembrane domain spans residues: 526-544
Download files:
KSHV_ORF4_rank_001.pdb
KSHV_ORF4_rank_002.pdb
KSHV_ORF4_rank_003.pdb
KSHV_ORF4_rank_004.pdb
KSHV_ORF4_rank_005.pdb
KSHV_ORF4_coverage.png
KSHV_ORF4_plddt.png
KSHV_ORF4_pae.png
KSHV_ORF4-nosignal_rank_001.pdb
KSHV_ORF4-nosignal_rank_002.pdb
KSHV_ORF4-nosignal_rank_003.pdb
KSHV_ORF4-nosignal_rank_004.pdb
KSHV_ORF4-nosignal_rank_005.pdb
Search for similar structures using Foldseek:
This page uses 3Dmol.js: Molecular visualization with WebGL by Nicholas Rego and David Koes.
Bioinformatics (2015) doi: 10.1093/bioinformatics/btu829
Predictions were run with Colabfold by the Steinegger lab:
Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. “ColabFold: Making protein folding accessible to all”.
Nature Methods (2022) doi: 10.1038/s41592-022-01488-1
Foldseek is developed by the Steinegger lab:
van Kempen M, Kim S, Tumescheit C, Mirdita M, Söding J, and Steinegger M. “Foldseek: fast and accurate protein structure search”.
bioRxiv (2022) doi: 10.1101/2022.02.07.479398
Alphafold2 was developed by Deepmind:
Jumper et al. “Highly accurate protein structure prediction with AlphaFold.”
Nature (2021) doi: 10.1038/s41586-021-03819-2
Signal peptide predictions were performed with DeepTMHMM
Jeppe Hallgren, Konstantinos D. Tsirigos, Mads Damgaard Pedersen, José Juan Almagro Armenteros, Paolo Marcatili, Henrik Nielsen, Anders Krogh, Ole Winther. “DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks.”
bioRxiv (2022) doi: 10.1101/2022.04.08.487609
AlphaFold3 models were generated through the Alphafold Server, which uses Google DeepMind’s AlphaFold technology
Abramson, J et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature (2024).
Nature (2021) doi: 10.1038/s41586-024-07487-w