4N5Z: Hemagglutinin HA1 chain

Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/Viet Nam/1203/2004 (H5N1). Determined by X-ray diffraction at 2.95 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Influenza A virus
Chains: 30
Atoms: 60,979
Mol. weight: 895.89 kDa
Ligands: NAG
Released: 20 Nov 2013

Explore 4N5Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4N5Z contains 241 α-helices and 711 β-strands across 30 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: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12-17	6	54
β-strand	18	1	212
β-strand	24-26	3	213
β-strand	34-36	3	213
β-strand	39-41	3	214
β-strand	43-44	2	215
β-strand	51-54	4	216
β-strand	56	1	216
α-helix	57-58	2
β-strand	59-60	2	217
β-strand	64	1	218
α-helix	66-71	6
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	217
β-strand	95	1	218
β-strand	100-102	3	219
α-helix	105-112	8
β-strand	115-122	8	219
α-helix	125A-126	3
β-strand	131	1	220
β-strand	136-140	5	221
β-strand	145-146	2	221
β-strand	151-153	3	219
β-strand	155	1	220
β-strand	157	1	222
β-strand	160	1	222
α-helix	162-163	2
β-strand	164-169	6	223
β-strand	176-184	9	219
α-helix	188-195	8
β-strand	202-205	4	223
β-strand	210-213	4	223
β-strand	223	1	224
β-strand	226	1	224
β-strand	229-237	9	219
α-helix	238	1
β-strand	242-247	6	223
β-strand	251-254	4	219
β-strand	256-262	8	219
β-strand	267-269	3	217
β-strand	274-279	6	216
β-strand	281-283	3	225
β-strand	286-287	2	225
β-strand	294-295	2	215
β-strand	302-303	2	225
α-helix	306	1
β-strand	307-308	2	215
β-strand	315-317	3	214
β-strand	321	1	213

Chain A: 11 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
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
α-helix	57-58	2
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	10
α-helix	105-112	8
β-strand	115-117	3	11
β-strand	120-122	3	10
α-helix	125A-126	3
β-strand	131	1	12
α-helix	132-133A	3
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	10
β-strand	155	1	12
β-strand	157	1	14
β-strand	160	1	14
α-helix	162-163	2
β-strand	164-169	6	15
β-strand	176-184	9	10
α-helix	188-195	8
β-strand	202-205	4	15
β-strand	210-213	4	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	10
β-strand	242-247	6	15
β-strand	251-254	4	10
β-strand	256-259	4	10
β-strand	261-262	2	11
β-strand	267-269	3	8
β-strand	274-279	6	7
β-strand	281-283	3	17
β-strand	286-287	2	17
β-strand	294-295	2	6
β-strand	302-303	2	17
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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	53
β-strand	10	1	53
β-strand	14	1	212
β-strand	22-27	6	54
β-strand	32-36	5	54
α-helix	40-58	19
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	54
β-strand	137-140	4	54
α-helix	146-153	8
α-helix	159-175	17

Chains B, d, F, J, L, N, P, R, T and X: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	240
β-strand	10	1	240
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	32-36	5	1
α-helix	38-58	21
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	159-175	17

Chain c: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12-17	6	72
β-strand	18	1	226
β-strand	24-26	3	227
β-strand	34-36	3	227
β-strand	39-41	3	228
β-strand	43-44	2	229
β-strand	51-54	4	230
β-strand	56	1	230
α-helix	57-58	2
β-strand	59-60	2	231
β-strand	64	1	232
α-helix	66-71	6
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	231
β-strand	95	1	232
β-strand	100-102	3	233
α-helix	105-112	8
β-strand	115-122	8	233
α-helix	125A-126	3
β-strand	131	1	234
α-helix	132-133A	3
β-strand	136-142	7	235
β-strand	144-146	3	235
β-strand	151-153	3	233
β-strand	155	1	234
β-strand	157	1	236
β-strand	160	1	236
α-helix	162-163	2
β-strand	164-169	6	237
β-strand	176-184	9	233
α-helix	188-195	8
β-strand	202-205	4	237
β-strand	210-213	4	237
β-strand	223	1	238
β-strand	226	1	238
β-strand	229-237	9	233
α-helix	238	1
β-strand	242-247	6	237
β-strand	251-254	4	233
β-strand	256-262	8	233
β-strand	267-269	3	231
β-strand	274-279	6	230
β-strand	281-282	2	239
β-strand	294-295	2	229
β-strand	302-303	2	239
α-helix	306	1
β-strand	307-308	2	229
β-strand	315-317	3	228
β-strand	321	1	227

Chain C: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	20
β-strand	18	1	21
β-strand	24-26	3	22
β-strand	34-36	3	22
β-strand	39-41	3	23
β-strand	43-44	2	24
β-strand	51-54	4	25
β-strand	56	1	25
α-helix	57-58	2
β-strand	59-60	2	26
β-strand	64	1	27
α-helix	66-71	6
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	26
β-strand	95	1	27
β-strand	100-102	3	28
α-helix	105-112	8
β-strand	115-122	8	28
α-helix	125A-126	3
β-strand	131	1	29
α-helix	132-133A	3
β-strand	136-140	5	30
β-strand	145-146	2	30
β-strand	151-153	3	28
β-strand	155	1	29
β-strand	157	1	31
β-strand	160	1	31
α-helix	162-163	2
β-strand	164-169	6	32
β-strand	176-184	9	28
α-helix	188-195	8
β-strand	202-205	4	32
β-strand	210-213	4	32
β-strand	223	1	33
β-strand	226	1	33
β-strand	229-237	9	28
β-strand	242-247	6	32
β-strand	251-254	4	28
β-strand	256-262	8	28
β-strand	267-269	3	26
β-strand	274-279	6	25
β-strand	281-283	3	34
β-strand	286-287	2	34
β-strand	294-295	2	24
β-strand	302-303	2	34
α-helix	306	1
β-strand	307-308	2	24
β-strand	315-317	3	23
β-strand	321	1	22

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	241
β-strand	10	1	241
β-strand	14	1	21
β-strand	22-27	6	20
β-strand	32-36	5	20
α-helix	38-58	21
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	20
β-strand	137-140	4	20
α-helix	146-154	9
α-helix	159-174	16

Chain E: 11 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12-17	6	37
β-strand	18	1	38
β-strand	25-26	2	39
β-strand	34-35	2	39
β-strand	36	1	40
β-strand	39-41	3	41
β-strand	43-44	2	42
β-strand	51-54	4	43
β-strand	56	1	43
α-helix	57-58	2
β-strand	59-60	2	44
β-strand	64	1	45
α-helix	66-71	6
α-helix	74-79	6
α-helix	82-83A	3
β-strand	87-89	3	44
β-strand	95	1	45
β-strand	100-102	3	46
α-helix	105-112	8
β-strand	115-122	8	46
α-helix	125A-126	3
β-strand	131	1	47
α-helix	132-133A	3
β-strand	136-140	5	48
β-strand	145-146	2	48
β-strand	151-153	3	46
β-strand	155	1	47
β-strand	157	1	49
β-strand	160	1	49
α-helix	162-163	2
β-strand	164-169	6	50
β-strand	176-184	9	46
α-helix	188-195	8
β-strand	202-205	4	50
β-strand	210-213	4	50
β-strand	223	1	51
β-strand	226	1	51
β-strand	229-237	9	46
β-strand	242-247	6	50
β-strand	251-254	4	46
β-strand	256-262	8	46
β-strand	267-269	3	44
β-strand	274-279	6	43
β-strand	281-283	3	52
β-strand	286-287	2	52
β-strand	294-295	2	42
β-strand	302-303	2	52
α-helix	306	1
β-strand	307-308	2	42
β-strand	315-317	3	41
β-strand	321	1	40

13 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c	protein	334	Influenza A virus	Q5EP31
Hemagglutinin	B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d	protein	181	Influenza A virus	Q6DQ33

Sequence of entity 1 (A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c), FASTA

>4N5Z_1 Hemagglutinin HA1 chain (chains A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS
VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI
IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLW
GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPN
DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
LTIGECPKYVKSNRLVLAIGLRNSPQRERRRKKR

Sequence of entity 2 (B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d), FASTA

>4N5Z_2 Hemagglutinin (chains B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGRLVP
R

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses. de Vries, R.P., Zhu, X., McBride, R. et al. J Virol (2014) 88:768-773. DOI 10.1128/JVI.02690-13 · 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…
9PHT 2.76 Å, Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in…

Browse structure collections

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