6E3H: S9-3-37

Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin. Determined by X-ray diffraction at 2.9 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 4
Atoms: 7,554
Mol. weight: 108.45 kDa
Ligands: NAG
Released: 26 Sept 2018

Explore 6E3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6E3H contains 23 α-helices and 95 β-strands across 4 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: 6 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	18	1	2
β-strand	25-28	4	3
β-strand	31-35	5	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	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
β-strand	84	1	10
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	11
α-helix	105-111	7
β-strand	115	1	10
β-strand	117-122	6	11
α-helix	125A-126	3
β-strand	131	1	12
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	11
β-strand	155	1	12
α-helix	162-163	2
β-strand	164-169	6	14
β-strand	175-184	10	11
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	11
β-strand	242-247	6	14
β-strand	251-254	4	11
β-strand	256-260A	6	11
β-strand	267-269	3	8
β-strand	274-279	6	7
β-strand	281-283	3	16
β-strand	286-287	2	16
β-strand	294-295	2	6
β-strand	302-304	3	16
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	17
β-strand	10	1	17
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	32-36	5	1
α-helix	38-57	20
β-strand	63-65	3	16
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	159-173	15

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	24
α-helix	7-9	3
β-strand	10-12	3	25
β-strand	18-25	8	24
α-helix	29-31	3
β-strand	33-39	7	25
β-strand	46-52	7	25
β-strand	57-59	3	25
β-strand	67-72	6	24
β-strand	77-82	6	24
β-strand	88-95	8	25
β-strand	103	1	25
β-strand	107-111	5	25
β-strand	117	1	26
α-helix	118-119	2
β-strand	120-124	5	27
β-strand	135-145	11	27
β-strand	146	1	26
β-strand	151-154	4	28
α-helix	155-157	3
β-strand	159	1	28
β-strand	163-165	3	27
α-helix	166-168	3
β-strand	169-170	2	27
β-strand	176-185	10	27
α-helix	186-188	3
β-strand	189	1	29
β-strand	192	1	29
β-strand	194-200	7	28
β-strand	205-211	7	28

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
β-strand	30	1	20
β-strand	31	1	20
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
β-strand	97-98	2	19
β-strand	102-106	5	19
β-strand	111	1	21
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-154	2	23
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-186	4
β-strand	191-197	7	23
β-strand	205-210	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A	protein	324	Influenza A virus	Q6DQ33
Hemagglutinin HA2	B	protein	175	Influenza A virus	Q6DQ18
antibody S9-3-37 light chain	L	protein	219	Homo sapiens
antibody S9-3-37 heavy chain	H	protein	233	Homo sapiens

Sequence of entity 1 (A), FASTA

>6E3H_1 Hemagglutinin HA1 (chains A)
GDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAG
WLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPK
SSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKNSTYPTIKRSYNNTNQEDLLVLWGIH
HPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVNGQSGRMEFFWTILKPNDAI
NFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTI
GECPKYVKSNRLVLATGLRNSPQR

Sequence of entity 2 (B), FASTA

>6E3H_2 Hemagglutinin HA2 (chains B)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISS

Sequence of entity 3 (L), FASTA

>6E3H_3 antibody S9-3-37 light chain (chains L)
DVVLTQTPLSSPVTRGQAASISCRSSQSLVHSDGNTYLSWIHQRPGQPPRLLIYKISKRF
SGVPDRISGSGAGTEFTLTISRVEADDVGMYYCTQASQFPRTFGQGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (H), FASTA

>6E3H_4 antibody S9-3-37 heavy chain (chains H)
QAQLVQSATEVKKPGASVKVSCQASGFTFTSYGFSWVRQAPGQGLEWMGWISAYDAKTKF
AEKFQDRVTMSIDTRTTTAYMEMRNLRFDDTAIYFCAREFRTQIVLGYFDWLEGNAFDMW
GQGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Ligands and cofactors

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

Primary citation

The D3-9 gene segment encodes for recurring and adaptable binding motifs in broadly neutralizing antibodies to influenza virus. Wu, N.C., Yamayoshi, S., Ito, M. et al. Cell Host Microbe (2018).

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…
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…
6E7G 3.09 Å, Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1…

Browse structure collections

About this viewer

MolViewer shows 6E3H 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.