6XPY: Human antibody S1V2-58

Human antibody S1V2-58 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2). Determined by X-ray diffraction at 3.6 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 3.6 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 3
Atoms: 5,568
Mol. weight: 82.71 kDa
Released: 19 May 2021

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

Secondary structure: helices and β-sheets

6XPY contains 19 α-helices and 77 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: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	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	130-131	2	6
β-strand	136-140	5	7
β-strand	145-146	2	7
β-strand	151-153	3	5
β-strand	155-156	2	6
α-helix	162-163	2
β-strand	164-168	5	8
β-strand	175-184	10	5
α-helix	188-195	8
β-strand	202-205	4	8
β-strand	210-213	4	8
β-strand	229-237	9	5
β-strand	243-247	5	8
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	281-283	3	9
β-strand	286-288	3	9
β-strand	294-295	2	1
β-strand	302	1	9
α-helix	306	1
β-strand	307-308	2	1

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	16
β-strand	7	1	17
β-strand	11-12	2	18
β-strand	18-23	6	17
β-strand	32-39	8	19
β-strand	45-52	8	19
β-strand	57-59	3	19
β-strand	67-69	3	17
β-strand	72	1	17
β-strand	77-82	6	17
α-helix	87-89	3
β-strand	91-101	11	19
β-strand	111-117	7	19
β-strand	118	1	16
β-strand	121-123	3	19
β-strand	124-125	2	18
α-helix	129-130	2
β-strand	131	1	20
β-strand	134-138	5	21
α-helix	142-144	3
β-strand	145-146	2	21
β-strand	149-159	11	21
β-strand	160	1	20
β-strand	165-168	4	22
α-helix	169-171	3
β-strand	177-179	3	21
α-helix	180-182	3
β-strand	183-184	2	21
β-strand	190-199	10	21
α-helix	200-202	3
β-strand	208-214	7	22
β-strand	219-225	7	22

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-12	3	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
β-strand	85-90	6	11
α-helix	97	1
β-strand	98	1	11
α-helix	99	1
β-strand	102-105	4	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	144-150	7	14
β-strand	154-155	2	14
β-strand	159-163	5	13
β-strand	167	1	15
β-strand	172	1	15
β-strand	173-182	10	13
α-helix	183-187	5
β-strand	192-198	7	14
β-strand	205-209	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	291	Influenza A virus	R4L1D1
Fab light chain	C	protein	214	Homo sapiens
Fab heavy chain	B	protein	238	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XPY_1 Hemagglutinin (chains A)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (C), FASTA

>6XPY_2 Fab light chain (chains C)
DIQMTQSPSSVSASLGDRVTLTCRASQPIRSYLNWYQHKPGLAPKLLVYAVSNLQSGVPS
RFSGSGSGTDFTLTVSSLQPEDFATYYCQQSYSTPYTFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>6XPY_3 Fab heavy chain (chains B)
QVQLQESGPGLVKPSETLSLTCTVSGGSLSIYYWSWVRQSPGKGLEWIGYISNSGSPTYH
PSLKSRVTISLDTSKSQFSLKLTSVTAADTALYFCARGVLEQLAPDFDSYYYGMNVWGQG
TTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

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…
6XPR 4.09 Å, Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain…
6XPQ 4.2 Å, Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of…

Browse structure collections

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