9PHS: Hemagglutinin

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor cyclic peptide CP141085 (CP1). Determined by X-ray diffraction at 2.02 Å resolution. Released 24 Dec 2025.

Method: X-ray diffraction
Resolution: 2.02 Å
Organisms: Influenza A virus (A/Puerto Rico/8/1934(H1N1)), synthetic construct
Chains: 9
Atoms: 12,840
Mol. weight: 179.97 kDa
Ligands: CA, NAG
Released: 24 Dec 2025

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

Secondary structure: helices and β-sheets

9PHS contains 41 α-helices and 165 β-strands across 9 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: 9 helices, 44 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	50-54	5	7
β-strand	56	1	7
α-helix	57-58	2
β-strand	59-62	4	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	10
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	102	1	10
α-helix	105-112	8
β-strand	115-122	8	10
α-helix	125A-126	4
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	157	1	13
β-strand	160	1	13
β-strand	164-169	6	14
β-strand	176-184	9	10
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	229-237	9	10
α-helix	238	1
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-262	7	10
β-strand	267-269	3	8
α-helix	272	1
β-strand	273-279	7	7
β-strand	281-283	3	16
β-strand	286-288	3	16
β-strand	294-295	2	6
β-strand	301	1	17
β-strand	302-303	2	16
β-strand	305	1	18
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
β-strand	321	1	4

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	19
β-strand	10	1	19
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-59	22
β-strand	62	1	18
β-strand	65	1	17
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	159-170	12

Chain C: 9 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	20
β-strand	18	1	21
β-strand	25-26	2	22
β-strand	34-35	2	22
β-strand	36	1	23
β-strand	39-41	3	24
β-strand	43-44	2	25
β-strand	50-54	5	26
β-strand	56	1	26
α-helix	57-58	2
β-strand	59-62	4	27
β-strand	64	1	28
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	29
β-strand	87-89	3	27
β-strand	95	1	28
β-strand	102	1	29
α-helix	105-112	8
β-strand	115-122	8	29
α-helix	125A-126	4
β-strand	131	1	30
β-strand	136-141	6	31
β-strand	144-146	3	31
β-strand	151-153	3	29
β-strand	155	1	30
β-strand	157	1	32
β-strand	160	1	32
β-strand	164-169	6	33
β-strand	176-184	9	29
α-helix	188-195	8
β-strand	202-205	4	33
β-strand	210-213	4	33
α-helix	219-222	4
β-strand	223	1	34
β-strand	226	1	34
β-strand	229-237	9	29
α-helix	238	1
β-strand	242-247	6	33
β-strand	251-254	4	29
β-strand	256-262	7	29
β-strand	267-269	3	27
β-strand	273-279	7	26
β-strand	281-283	3	35
β-strand	286-287	2	35
β-strand	294-295	2	25
β-strand	301	1	36
β-strand	302-303	2	35
β-strand	305	1	37
α-helix	306	1
β-strand	307-308	2	25
β-strand	315-317	3	24
β-strand	321	1	23

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	38
β-strand	10	1	38
β-strand	14	1	21
β-strand	22-28	7	20
β-strand	31-36	6	20
α-helix	38-58	21
β-strand	62	1	37
β-strand	65	1	36
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-134	5	20
β-strand	137-140	4	20
α-helix	146-153	8
α-helix	160-170	11

Chain E: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	39
β-strand	18	1	40
β-strand	25-26	2	41
β-strand	34-35	2	41
β-strand	36	1	42
β-strand	39-41	3	43
β-strand	43-44	2	44
β-strand	50-54	5	45
β-strand	56	1	45
α-helix	57-58	2
β-strand	59-60	2	46
β-strand	64	1	47
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	48
β-strand	87-89	3	46
β-strand	95	1	47
β-strand	102	1	48
α-helix	105-112	8
β-strand	115-122	8	48
α-helix	125A-126	4
β-strand	131	1	49
β-strand	136-141	6	50
β-strand	144-146	3	50
β-strand	151-153	3	48
β-strand	155	1	49
β-strand	157	1	51
β-strand	160	1	51
β-strand	164-169	6	52
β-strand	176-184	9	48
α-helix	188-195	8
β-strand	202-205	4	52
β-strand	210-213	4	52
β-strand	223	1	53
β-strand	226	1	53
β-strand	229-237	9	48
α-helix	238	1
β-strand	242-247	6	52
β-strand	251-254	4	48
β-strand	256-262	7	48
β-strand	267-269	3	46
β-strand	273-279	7	45
β-strand	281-283	3	54
β-strand	286-288	3	54
β-strand	294-295	2	44
β-strand	301	1	55
β-strand	302-303	2	54
β-strand	305	1	56
α-helix	306	1
β-strand	307-308	2	44
β-strand	315-317	3	43
β-strand	321	1	42

Chain F: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	57
β-strand	10	1	57
β-strand	14	1	40
β-strand	22-28	7	39
β-strand	31-36	6	39
α-helix	38-58	21
β-strand	62	1	56
β-strand	65	1	55
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	39
β-strand	137-140	4	39
α-helix	146-153	8
α-helix	160-170	11

Chains G, H and K: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	58
β-strand	18	1	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E	protein	326	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	P03452 (AlphaFold model)
Hemagglutinin HA2 chain	B, D, F	protein	176	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	P03452 (AlphaFold model)
cyclic peptide CP141085	G, H, K	protein	19	synthetic construct

Sequence of entity 1 (A, C, E), FASTA

>9PHS_1 Hemagglutinin (chains A, C, E)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAGW
LLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPKE
SSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIHH
PPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTII
FEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIG
ECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 2 (B, D, F), FASTA

>9PHS_2 Hemagglutinin HA2 chain (chains B, D, F)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMN
IQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV

Sequence of entity 3 (G, H, K), FASTA

>9PHS_3 cyclic peptide CP141085 (chains G, H, K)
PPVSLYEDPLGVAGGMGVY

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Water and common crystallization additives (GOL) are not listed.

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 P03452 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PHD 1.59 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
5VLI 1.8 Å, Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza…
8VQQ 2.05 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
1RVX 2.2 Å, 1934 H1 Hemagglutinin in complex with LSTA
8VQM 2.21 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
8VQN 2.21 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
1RVZ 2.25 Å, 1934 H1 Hemagglutinin in complex with LSTC
5W5S 2.28 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
8VQL 2.29 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
1RU7 2.3 Å, 1934 Human H1 Hemagglutinin
9PIB 2.35 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
9DXX 2.37 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…

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