6XPR: Human antibody D2 H1-1/H3-1 H3

Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain of A/Texas/50/2012(H3N2). Determined by X-ray diffraction at 4.09 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 4.09 Å
Organisms: Influenza A virus (A/Texas/50/2012(H3N2)), Homo sapiens
Chains: 6
Atoms: 11,025
Mol. weight: 165.39 kDa
Ligands: NAG
Released: 19 May 2021

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

Secondary structure: helices and β-sheets

6XPR contains 35 α-helices and 140 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	51-54	4	1
β-strand	58-62	5	2
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	3
β-strand	86-89	4	2
β-strand	100-101	2	4
α-helix	105-115	11
β-strand	117	1	3
β-strand	120-122	3	4
β-strand	130-131	2	5
β-strand	136-141	6	6
β-strand	144-146	3	6
β-strand	151-153	3	4
β-strand	155-156	2	5
β-strand	157	1	7
β-strand	160	1	7
β-strand	164-168	5	8
β-strand	176-184	9	4
α-helix	188-195	8
β-strand	202-205	4	8
β-strand	210-213	4	8
β-strand	229-237	9	4
β-strand	243-247	5	8
β-strand	251-254	4	4
β-strand	256-259	4	4
β-strand	266-269	4	2
α-helix	272-273	2
β-strand	274-278	5	1
β-strand	281-283	3	9
β-strand	286-288	3	9
β-strand	302	1	9

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	12	1	11
β-strand	18-24	7	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-97	6	12
β-strand	100-102	3	13
β-strand	111-113	3	13
β-strand	117	1	12
β-strand	121-123	3	12
β-strand	125	1	11
β-strand	134-138	5	14
β-strand	145	1	15
β-strand	149	1	16
β-strand	150	1	15
β-strand	152-159	8	14
β-strand	164-168	5	17
α-helix	169-171	3
β-strand	173	1	17
β-strand	177-179	3	14
α-helix	180-182	3
β-strand	183-184	2	14
β-strand	190-196	7	14
β-strand	199	1	16
β-strand	209-214	6	17
α-helix	215-217	3
β-strand	219-224	6	17

Chain C: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10	1	19
β-strand	19-25	7	18
β-strand	33-38	6	19
β-strand	44-49	6	19
β-strand	53-54	2	19
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	85-90	6	19
β-strand	98	1	19
α-helix	99-101	3
β-strand	102-103	2	19
α-helix	111-113	3
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	20
β-strand	145-150	6	21
β-strand	154	1	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-186	4
β-strand	192-197	6	21
β-strand	205-209	5	21

Chain D: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	51-54	4	22
β-strand	58-60	3	23
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	24
β-strand	86-89	4	23
β-strand	101	1	25
α-helix	105-115	11
β-strand	117	1	24
β-strand	120-122	3	25
β-strand	130-131	2	26
β-strand	136-141	6	27
β-strand	144-146	3	27
β-strand	151-153	3	25
β-strand	155-156	2	26
β-strand	164-168	5	28
β-strand	175-184	10	25
α-helix	188-195	8
β-strand	202-205	4	28
β-strand	210-213	4	28
β-strand	229-237	9	25
β-strand	243-247	5	28
β-strand	251-254	4	25
β-strand	256-260	5	25
β-strand	266-269	4	23
α-helix	272-273	2
β-strand	274-278	5	22
β-strand	281-283	3	29
β-strand	286-287	2	29
β-strand	302-303	2	29

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	30
β-strand	11-12	2	31
β-strand	18-23	6	30
α-helix	29-31	3
β-strand	34-39	6	32
β-strand	45-51	7	32
β-strand	58-60	3	32
α-helix	62-64	3
β-strand	68-73	6	30
β-strand	78-83	6	30
α-helix	88-90	3
β-strand	92-97	6	32
β-strand	100-102	3	33
β-strand	111-113	3	33
β-strand	121-123	3	32
β-strand	124-125	2	31
α-helix	128-130	3
β-strand	131	1	34
β-strand	134-138	5	35
β-strand	149-159	11	35
β-strand	160	1	34
β-strand	165-168	4	36
α-helix	169-171	3
β-strand	177-179	3	35
α-helix	180-182	3
β-strand	183-184	2	35
β-strand	190-199	10	35
β-strand	209-214	6	36
α-helix	215-217	3
β-strand	219-224	6	36

Chain F: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	10-12	3	38
β-strand	19-25	7	37
β-strand	33-38	6	38
β-strand	44-49	6	38
β-strand	53-54	2	38
β-strand	62-67	6	37
β-strand	70-75	6	37
α-helix	80-82	3
β-strand	85-90	6	38
β-strand	98	1	38
β-strand	103-105	3	38
β-strand	114-118	5	39
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	39
β-strand	145-150	6	40
β-strand	154-155	2	40
β-strand	159-163	5	39
α-helix	164-167	4
β-strand	173-182	10	39
α-helix	183-187	5
β-strand	192-197	6	40
β-strand	205-209	5	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, D	protein	291	Influenza A virus (A/Texas/50/2012(H3N2))	R4L1D1
antibody D2 H1-1/H3-1 H3 heavy chain	B, E	protein	238	Homo sapiens
antibody D2 H1-1/H3-1 H3 light chain	C, F	protein	214	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>6XPR_1 Hemagglutinin (chains A, D)
TNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSN
CYPYDVPDYASLRSLVASSGTLEFNNESFNWNGVTQNGTSSACIRRSNNSFFSRLNWLTH
LNFKYPALNVTMPNNEQFDKLYIWGVHHPVTDKDQIFLYAQPSGRITVSTKRSQQAVIPN
IGFRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGK
CKSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGGALEVLFQ

Sequence of entity 2 (B, E), FASTA

>6XPR_2 antibody D2 H1-1/H3-1 H3 heavy chain (chains B, E)
QVQLVQSGGGLVRPGGSLRLSCAASGFTFSSAWMTWVRQAPGKGLEWVANIKEDGSEKYY
VDSVKGRFSISRDNAKNSLYLQISSLRAEDTAVYYCARRFVERLWGQSKPYDAVDIWGQG
TMVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Sequence of entity 3 (C, F), FASTA

>6XPR_3 antibody D2 H1-1/H3-1 H3 light chain (chains C, F)
DIQMTQSPSSLSASVGDRVTITCRASQSISNYLNWYQQKPGKAPKLLIYVASNLQSGVPS
RFSGSGSGTDFALTISSLQPEDFASYYCQQSYSPVTTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

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

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