6XPQ: Human antibody D1 H1-17/H3-14

Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2). Determined by X-ray diffraction at 4.2 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 4.2 Å
Organisms: Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
Chains: 3
Atoms: 5,543
Mol. weight: 84.18 kDa
Released: 19 May 2021

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

Secondary structure: helices and β-sheets

6XPQ contains 13 α-helices and 70 β-strands across 3 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	43-44	2	1
β-strand	51-54	4	2
β-strand	58-60	3	3
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	4
β-strand	86-89	4	3
β-strand	101	1	5
α-helix	105-115	11
β-strand	117	1	4
β-strand	120-122	3	5
β-strand	131	1	6
β-strand	136-141	6	7
β-strand	144-146	3	7
β-strand	151-153	3	5
β-strand	155	1	6
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-169	6	9
β-strand	175-184	10	5
α-helix	188-195	8
β-strand	202-205	4	9
β-strand	210-213	4	9
β-strand	229-237	9	5
β-strand	242-247	6	9
β-strand	251-254	4	5
β-strand	256-260	5	5
β-strand	266-269	4	3
β-strand	274-278	5	2
β-strand	282-283	2	10
β-strand	286-287	2	10
β-strand	294-295	2	1
β-strand	302	1	10
α-helix	306	1
β-strand	307-308	2	1

Chain B: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	11	1	17
β-strand	18-25	8	16
β-strand	35-42	8	18
β-strand	46-54	9	18
β-strand	59-61	3	18
β-strand	69-74	6	16
β-strand	79-84	6	16
α-helix	89-91	3
β-strand	93-102	10	18
β-strand	111-116	6	18
β-strand	120-122	3	18
β-strand	123	1	17
β-strand	133-137	5	19
β-strand	148-156	9	19
β-strand	164-167	4	20
α-helix	168-170	3
β-strand	176-178	3	19
α-helix	179-181	3
β-strand	182-183	2	19
β-strand	189-198	10	19
β-strand	208-213	6	20
β-strand	218-223	6	20

Chain C: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	12-13	2	12
β-strand	19-25	7	11
β-strand	34-38	5	13
β-strand	45-49	5	13
β-strand	53-54	2	13
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	95-96	2	13
β-strand	100-102	3	13
β-strand	103-104	2	12
α-helix	105-106	2
β-strand	112-116	5	14
α-helix	117-119	3
α-helix	120-124	5
β-strand	127-137	11	14
β-strand	143-148	6	15
β-strand	152-153	2	15
β-strand	157-162	6	14
β-strand	171-180	10	14
α-helix	181-185	5
β-strand	190-195	6	15
β-strand	203-207	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	291	Influenza A virus (A/Texas/50/2012(H3N2))	R4L1D1
antibody D1 H1-17/H3-14 light chain	C	protein	212	Homo sapiens
antibody D1 H1-17/H3-14 heavy chain	B	protein	250	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XPQ_1 Hemagglutinin (chains A)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (C), FASTA

>6XPQ_2 antibody  D1 H1-17/H3-14 light chain (chains C)
DIRVTQSPSSLSASVGDRVTITCRASQSISRSLNWYQQRPGKAPKFLIYAASNLQSGVPS
RFSGGGSGTDFTLTISSLQPEDFATYYCQETYSRTFGQGTKADIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLS
KADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>6XPQ_3 antibody D1 H1-17/H3-14 heavy chain (chains B)
QVQLQESGPGLVKPSESLSLTCSVSGGSVSSNLHYWSWIRQLPGKGLEWIGYISYTGSTK
YNPSLNGRVTLSIDASKNQFSLELSSVTAADTAVYYCARDFFEKLIADDLNAFDIWGQGT
MVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEVLFQ
GPLGHHHHHH

Primary citation

A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface. McCarthy, K.R., Lee, J., Watanabe, A. et al. mBio (2021) 12:e0114421-e0114421. DOI 10.1128/mBio.01144-21 · PubMed

Other PDB entries of the same protein (UniProt R4L1D1), best resolution first:

6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
5W08 2.6 Å, A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab
6XQ2 3.0 Å, Human antibody S8V2-37 in complex with the influenza hemagglutinin head domain of…
6XPY 3.6 Å, Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of…
6XPR 4.09 Å, Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain…

Browse structure collections

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