9PHT: Hemagglutinin

Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141085 (CP1). Determined by X-ray diffraction at 2.76 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.76 Å
Organisms: Influenza A virus (A/Viet Nam/1203/2004(H5N1)), synthetic construct
Chains: 3
Atoms: 4,232
Mol. weight: 60.73 kDa
Ligands: NAG
Released: 24 Dec 2025

Explore 9PHT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PHT contains 16 α-helices and 48 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	18	1	2
β-strand	25-26	2	3
β-strand	34-35	2	3
β-strand	36	1	4
β-strand	39-41	3	5
β-strand	43-44	2	6
β-strand	51-54	4	7
β-strand	56	1	7
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	10
α-helix	105-112	8
β-strand	115-122	8	10
α-helix	125A-126	3
β-strand	131	1	11
β-strand	136-141	6	12
β-strand	144-146	3	12
β-strand	151-153	3	10
β-strand	155	1	11
β-strand	164-169	6	13
β-strand	176-184	9	10
α-helix	188-195	8
β-strand	202-205	4	13
β-strand	210-213	4	13
α-helix	215-217	3
β-strand	223	1	14
β-strand	226	1	14
β-strand	229-237	9	10
α-helix	238	1
β-strand	242-247	6	13
β-strand	251-254	4	10
β-strand	256-262	8	10
β-strand	267-269	3	8
β-strand	274-279	6	7
β-strand	281-283	3	15
β-strand	286-287	2	15
β-strand	294-295	2	6
β-strand	302-303	2	15
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
α-helix	320	1
β-strand	321	1	4
α-helix	322-323	2

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	16
β-strand	10	1	16
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-58	21
α-helix	59-61	3
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	163-173	11

Chain G: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	17
β-strand	18	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q5EP31
Hemagglutinin	B	protein	175	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q5EP31
cyclic peptide CP141085	G	protein	19	synthetic construct

Sequence of entity 1 (A), FASTA

>9PHT_1 Hemagglutinin (chains A)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS
VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI
IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLW
GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPN
DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
LTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

Sequence of entity 2 (B), FASTA

>9PHT_2 Hemagglutinin (chains B)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISS

Sequence of entity 3 (G), FASTA

>9PHT_3 cyclic peptide CP141085 (chains G)
PPVSLYEDPLGVAGGMGVY

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

V H H antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion. Kadam, R.U., Juraszek, J., Brandenburg, B. et al. Npj Viruses (2025) 3:83-83. DOI 10.1038/s44298-025-00166-1 · PubMed

Other PDB entries of the same protein (UniProt Q5EP31), best resolution first:

4BH4 1.9 Å, Haemagglutinin from a Transmissible Mutant H5 Influenza Virus in Complex with Avian…
4BH3 2.0 Å, Haemagglutinin from a Transmissible Mutant H5 Influenza Virus in Complex with Human…
4BH2 2.12 Å, Crystal Structure of the Haemagglutinin from a Transmissible Mutant H5 Influenza Virus
6CFG 2.32 Å, Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in…
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…

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