diff --git a/alphapulldown/folding_backend/alphafold3_backend.py b/alphapulldown/folding_backend/alphafold3_backend.py
index e58d2dcd..4b2341b9 100644
--- a/alphapulldown/folding_backend/alphafold3_backend.py
+++ b/alphapulldown/folding_backend/alphafold3_backend.py
@@ -804,8 +804,8 @@ def _process_single_object(obj, chain_id_counter_ref, used_chain_ids: set):
                                 id=base_chain.id,
                                 sequence=base_chain.sequence,
                                 ptms=base_chain.ptms,
-                                unpaired_msa=a3m_sliced,
-                                paired_msa='',
+                                unpaired_msa='',
+                                paired_msa=a3m_sliced,
                                 templates=base_chain.templates,
                             )
                             custom_unpaired_chain_ids.add(base_chain.id)