9PIB: Hemagglutinin

Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with fusion inhibitor CLIPS peptide CP121132 (CP-S1). Determined by X-ray diffraction at 2.35 Å resolution. Released 18 Mar 2026.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Influenza A virus (A/Puerto Rico/8/1934(H1N1)), synthetic construct
Chains: 12
Atoms: 17,374
Mol. weight: 238.76 kDa
Ligands: FUC, NAG, SEZ
Released: 18 Mar 2026

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

Secondary structure: helices and β-sheets

9PIB contains 53 α-helices and 206 β-strands across 8 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: 8 helices, 43 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	51-53	3	7
β-strand	54	1	8
β-strand	56	1	8
α-helix	57-58	2
β-strand	59-60	2	9
β-strand	64	1	10
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	11
β-strand	87-89	3	9
β-strand	95	1	10
β-strand	102	1	11
α-helix	105-112	8
β-strand	115-122	8	11
α-helix	125A-126	4
β-strand	131	1	12
β-strand	136-141	6	13
β-strand	144-146	3	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	157	1	14
β-strand	160	1	14
β-strand	164-169	6	15
β-strand	176-184	9	11
α-helix	188-195	8
β-strand	202-205	4	15
β-strand	210-213	4	15
α-helix	219-222	4
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	256-262	7	11
β-strand	267-269	3	9
β-strand	274-278	5	7
β-strand	281-283	3	17
β-strand	286-288	3	17
β-strand	294-295	2	6
β-strand	301-305	5	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, 8 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	38-58	21
β-strand	62-65	4	18
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: 8 helices, 42 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	51-54	4	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	202-206	5	33
β-strand	209-213	5	33
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	274-279	6	26
β-strand	281-282	2	34
β-strand	287-288	2	34
β-strand	294-295	2	25
β-strand	301	1	35
β-strand	302-303	2	34
β-strand	305	1	36
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	37
β-strand	10	1	37
β-strand	14	1	21
β-strand	22-27	6	20
β-strand	32-36	5	20
α-helix	38-58	21
β-strand	62	1	36
β-strand	65	1	35
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	20
β-strand	137-140	4	20
α-helix	146-153	8
α-helix	159-170	12

Chain E: 7 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	38
β-strand	18	1	39
β-strand	24-26	3	40
β-strand	34-36	3	40
β-strand	39-41	3	41
β-strand	43-44	2	42
β-strand	50-53	4	43
β-strand	54	1	44
β-strand	56	1	44
α-helix	57-58	2
β-strand	59-62	4	45
β-strand	64	1	46
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	47
β-strand	87-89	3	45
β-strand	95	1	46
β-strand	102	1	47
α-helix	105-112	8
β-strand	115-122	8	47
β-strand	131	1	48
β-strand	136-141	6	49
β-strand	144-146	3	49
β-strand	151-153	3	47
β-strand	155	1	48
β-strand	157	1	50
β-strand	160	1	50
β-strand	164-169	6	51
β-strand	176-184	9	47
α-helix	188-195	8
β-strand	202-206	5	51
β-strand	209-213	5	51
α-helix	220-222	3
β-strand	223	1	52
β-strand	226	1	52
β-strand	229-237	9	47
β-strand	242-247	6	51
β-strand	251-254	4	47
β-strand	256-262	7	47
β-strand	267-269	3	45
β-strand	273-278	6	43
β-strand	281-282	2	53
β-strand	287-288	2	53
β-strand	294-295	2	42
β-strand	301	1	54
β-strand	302-303	2	53
β-strand	305	1	55
α-helix	306	1
β-strand	307-308	2	42
β-strand	315-317	3	41
β-strand	321	1	40

Chain F: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	56
β-strand	10	1	56
β-strand	14	1	39
β-strand	22-28	7	38
β-strand	31-36	6	38
α-helix	38-58	21
α-helix	60-61	2
β-strand	62	1	55
β-strand	65	1	54
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	38
β-strand	137-140	4	38
α-helix	146-154	9
α-helix	159-169	11

Chain G: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	57
β-strand	18	1	58
β-strand	25-26	2	59
β-strand	34-35	2	59
β-strand	36	1	60
β-strand	39-41	3	61
β-strand	43-44	2	62
β-strand	51-54	4	63
β-strand	56	1	63
α-helix	57-58	2
β-strand	59-60	2	64
β-strand	64	1	65
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	66
β-strand	87-89	3	64
β-strand	95	1	65
β-strand	102	1	66
α-helix	105-112	8
β-strand	115-122	8	66
α-helix	125A-126	4
β-strand	131	1	67
β-strand	136-141	6	68
β-strand	144-146	3	68
β-strand	151-153	3	66
β-strand	155	1	67
β-strand	157	1	69
β-strand	160	1	69
β-strand	164-169	6	70
β-strand	176-184	9	66
α-helix	188-195	8
β-strand	202-205	4	70
β-strand	210-213	4	70
β-strand	229-237	9	66
α-helix	238	1
β-strand	242-247	6	70
β-strand	251-254	4	66
β-strand	256-262	7	66
β-strand	267-269	3	64
β-strand	274-279	6	63
β-strand	281-282	2	71
β-strand	287	1	71
β-strand	294-295	2	62
β-strand	301	1	72
β-strand	302-303	2	71
β-strand	305	1	73
α-helix	306	1
β-strand	307-308	2	62
β-strand	315-317	3	61
β-strand	321	1	60

Chain H: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	74
β-strand	10	1	74
β-strand	14	1	58
β-strand	22-27	6	57
β-strand	32-36	5	57
α-helix	38-57	20
β-strand	62	1	73
β-strand	65	1	72
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	57
β-strand	137-140	4	57
α-helix	146-153	8
α-helix	160-162	3
α-helix	163-170	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E, G	protein	326	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	P03452 (AlphaFold model)
Hemagglutinin HA2 chain	B, D, F, H	protein	176	Influenza A virus (A/Puerto Rico/8/1934(H1N1))	P03452 (AlphaFold model)
CLIPS peptide CP121132	N, O, P, Q	protein	13	synthetic construct

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

>9PIB_1 Hemagglutinin (chains A, C, E, G)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGIAPLQLGKCNIAGW
LLGNPECDPLLPVRSWSYIVETPNSENGICYPGDFIDYEELREQLSSVSSFERFEIFPKE
SSWPNHNTNGVTAACSHEGKSSFYRNLLWLTEKEGSYPKLKNSYVNKKGKEVLVLWGIHH
PPNSKEQQNLYQNENAYVSVVTSNYNRRFTPEIAERPKVRDQAGRMNYYWTLLKPGDTII
FEANGNLIAPMYAFALSRGFGSGIITSNASMHECNTKCQTPLGAINSSLPYQNIHPVTIG
ECPKYVRSAKLRMVTGLRNIPSIQSR

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

>9PIB_2 Hemagglutinin HA2 chain (chains B, D, F, H)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNTVIEKMN
IQFTAVGKEFNKLEKRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDNECMESVRNGTYDYPKYSEESKLNREKVDGV

Sequence of entity 3 (N, O, P, Q), FASTA

>9PIB_3 CLIPS peptide CP121132 (chains N, O, P, Q)
XRCLCYFEWLSCX

Ligands and cofactors

ID	Name	Formula	Copies
FUC	alpha-L-fucopyranose	C6 H12 O5	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
SEZ	1,3,5-trimethylbenzene	C9 H12	4

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

Primary citation

Small molecule-constrained paratope mimetic bicyclic peptides as potent inhibitors of group 1 and 2 influenza A virus hemagglutinins. Kadam, R.U., Juraszek, J., Brandenburg, B. et al. Proc Natl Acad Sci U S A (2026) 123:e2537533123-e2537533123. DOI 10.1073/pnas.2537533123 · 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…
9PHS 2.02 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…
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
9DXX 2.37 Å, Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in…

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