6E7G: Hemagglutinin HA1 chain

Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus. Determined by X-ray diffraction at 3.09 Å resolution. Released 19 Jun 2019.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Chains: 6
Atoms: 11,548
Mol. weight: 177.11 kDa
Ligands: NAG
Released: 19 Jun 2019

Explore 6E7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E7G contains 32 α-helices and 133 β-strands across 6 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: 5 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	25-26	2	2
β-strand	34-35	2	2
β-strand	36	1	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	51-54	4	6
β-strand	56	1	6
α-helix	57-58	2
β-strand	59-61	3	7
β-strand	64	1	8
α-helix	66-70	5
β-strand	84	1	9
β-strand	87-89	3	7
β-strand	95	1	8
β-strand	100-102	3	10
α-helix	105-111	7
β-strand	115	1	9
β-strand	117-122	6	10
β-strand	133A	1	11
β-strand	140-142	3	12
β-strand	144-145	2	12
β-strand	151-153	3	10
β-strand	154	1	11
β-strand	157	1	13
β-strand	160	1	13
β-strand	164-169	6	14
β-strand	175-184	10	10
α-helix	188-194	7
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	229-237	9	10
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-260A	6	10
β-strand	267-269	3	7
β-strand	274-279	6	6
β-strand	281-282	2	15
β-strand	288	1	15
β-strand	294-295	2	5
β-strand	302-303	2	15
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-57	20
β-strand	64-65	2	15
α-helix	72-74	3
α-helix	75-125	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	147-149	3
α-helix	150-154	5
α-helix	159-168	10

Chain C: 6 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	16
β-strand	25-26	2	17
β-strand	34-35	2	17
β-strand	36	1	18
β-strand	39-41	3	19
β-strand	43-44	2	20
β-strand	51-54	4	21
β-strand	56	1	21
α-helix	57-58	2
β-strand	59-61	3	22
β-strand	64	1	23
α-helix	66-70	5
β-strand	84	1	24
β-strand	87-89	3	22
β-strand	95	1	23
β-strand	102	1	25
α-helix	105-112	8
β-strand	115	1	24
β-strand	117-122	6	25
β-strand	133-134	3	25
β-strand	136-142	7	26
β-strand	144-146	3	26
β-strand	151-155	5	25
β-strand	157	1	27
β-strand	160	1	27
α-helix	162-163	2
β-strand	164-169	6	28
β-strand	175-184	10	25
α-helix	188-194	7
β-strand	202-205	4	28
β-strand	210-213	4	28
β-strand	229-237	9	25
β-strand	242-247	6	28
β-strand	251-254	4	25
β-strand	256-261A	6	25
β-strand	267-269	3	22
β-strand	274-279	6	21
β-strand	281-282	2	29
β-strand	288	1	29
β-strand	294-295	2	20
β-strand	302-304	3	29
α-helix	306	1
β-strand	307-308	2	20
β-strand	315-317	3	19
β-strand	321	1	18

Chain D: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	16
α-helix	38-57	20
β-strand	63-65	3	29
α-helix	72-74	3
α-helix	75-123	49
β-strand	131-132	2	30
β-strand	137	1	16
β-strand	138-139	2	30
α-helix	146-154	9
α-helix	163-169	7

Chain E: 6 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	15-17	3	31
β-strand	18	1	32
β-strand	25-26	2	33
β-strand	34-35	2	33
β-strand	36	1	34
β-strand	39-41	3	35
β-strand	43-44	2	36
β-strand	51-54	4	37
α-helix	57-58	2
β-strand	59-61	3	38
β-strand	64	1	39
α-helix	66-70	5
β-strand	84	1	40
β-strand	87-89	3	38
β-strand	95	1	39
β-strand	100-102	3	41
α-helix	105-112	8
β-strand	115	1	40
β-strand	117-122	6	41
α-helix	125A-126	3
β-strand	133	1	42
β-strand	136-140	5	43
β-strand	145-146	2	43
β-strand	151-153	3	41
β-strand	155	1	42
β-strand	157	1	44
β-strand	160	1	44
β-strand	164-169	6	45
β-strand	175-184	10	41
α-helix	188-194	7
β-strand	202-205	4	45
β-strand	210-213	4	45
β-strand	223	1	46
β-strand	226	1	46
β-strand	229-237	9	41
β-strand	242-247	6	45
β-strand	251-254	4	41
β-strand	256-260A	6	41
β-strand	267-269	3	38
β-strand	274-279	6	37
β-strand	281-282	2	47
β-strand	288	1	47
β-strand	294-295	2	36
β-strand	302-303	2	47
α-helix	306	1
β-strand	307-308	2	36
β-strand	315-317	3	35
β-strand	321	1	34

Chain F: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	32
β-strand	22-24	3	31
α-helix	38-57	20
α-helix	75-123	49
α-helix	150-154	5
α-helix	163-170	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A, C, E	protein	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ33
Hemagglutinin HA2 chain	B, D, F	protein	177	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Q6DQ18

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

>6E7G_1 Hemagglutinin HA1 chain (chains A, C, E)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCS
VAGWLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQI
IPKSSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTAPTIKRSYNNTNQEDLLVLW
GIHHPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPN
DAINFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHP
LTIGECPKYVKSNRLVLATGLRNSPQRERRRKKR

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

>6E7G_2 Hemagglutinin HA2 chain (chains B, D, F)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSGR

Ligands and cofactors

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

Primary citation

N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses. Broszeit, F., Tzarum, N., Zhu, X. et al. Cell Rep (2019) 27:3284-3294.e6. DOI 10.1016/j.celrep.2019.05.048 · PubMed

Other PDB entries of the same protein (UniProt Q6DQ33), best resolution first:

4FQI 1.71 Å, Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin
4XNQ 2.0 Å, Antibody hemagglutinin Complexes
6CF5 2.04 Å, Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in…
4KDO 2.4 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDN 2.48 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDM 2.5 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
4XNM 2.51 Å, Antibody Influenza H5 Complex
3GBM 2.7 Å, Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.
4XRC 2.74 Å, Antibody hemagglutinin Complexes
5A3I 2.89 Å, Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5…
6E3H 2.9 Å, Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…

Browse structure collections

About this viewer

MolViewer shows 6E7G directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.