6XPX: Human antibody S1V2-51

Human antibody S1V2-51 in complex with the influenza hemagglutinin head domain of A/Aichi/2/1968 (X-31)(H3N2). Determined by X-ray diffraction at 2.6 Å resolution. Released 19 May 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 3
Atoms: 5,535
Mol. weight: 82.53 kDa
Ligands: BCN, NAG
Released: 19 May 2021

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

Secondary structure: helices and β-sheets

6XPX contains 22 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: 7 helices, 32 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	100-101	2	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	1	7
α-helix	137-139	3
β-strand	146	1	7
β-strand	151-153	3	5
β-strand	155-156	2	6
β-strand	157	1	8
β-strand	160	1	8
β-strand	164-169	6	9
β-strand	176-184	9	5
α-helix	188-195	8
β-strand	201-205	5	9
β-strand	210-213	4	9
β-strand	223	1	10
β-strand	226	1	10
β-strand	229-237	9	5
β-strand	242-249	8	9
β-strand	251-254	4	5
β-strand	256-259	4	5
β-strand	266-269	4	3
α-helix	272-273	2
β-strand	274-278	5	2
β-strand	281-283	3	11
β-strand	286-288	3	11
β-strand	294-295	2	1
β-strand	302	1	11
α-helix	306	1
β-strand	307-308	2	1

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	46-51	6	19
β-strand	58-60	3	19
β-strand	68-73	6	18
β-strand	78-83	6	18
α-helix	88-90	3
β-strand	92-98	7	19
β-strand	105-106	2	19
β-strand	110-114	5	19
α-helix	117-119	3
β-strand	120	1	20
α-helix	121-122	2
β-strand	123-127	5	21
β-strand	138-148	11	21
β-strand	149	1	20
β-strand	154-157	4	22
β-strand	162	1	22
β-strand	166-168	3	21
α-helix	169-171	3
β-strand	172-173	2	21
β-strand	179-188	10	21
α-helix	189-191	3
β-strand	197-203	7	22
α-helix	204-206	3
β-strand	208-214	7	22

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
β-strand	30	1	14
β-strand	37	1	14
β-strand	39-44	6	13
β-strand	51-55	5	13
β-strand	59-60	2	13
α-helix	61	1
β-strand	68-72	5	12
β-strand	76-81	6	12
α-helix	86-88	3
β-strand	90-96	7	13
α-helix	102	1
β-strand	103-104	2	13
β-strand	108-112	5	13
β-strand	117	1	15
α-helix	118-119	2
β-strand	120-124	5	16
α-helix	125-127	3
α-helix	128-132	5
β-strand	135-145	11	16
β-strand	146	1	15
β-strand	151-156	6	17
β-strand	159-160	2	17
β-strand	165-169	5	16
α-helix	170-173	4
β-strand	179-188	10	16
α-helix	189-193	5
β-strand	198-203	6	17
β-strand	211-215	5	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A	protein	289	Influenza A virus	P03437
S1V2-51 Fab light chain	C	protein	220	Homo sapiens
S1V2-51 Fab heavy chain	B	protein	227	Homo sapiens

Sequence of entity 1 (A), FASTA

>6XPX_1 Hemagglutinin (chains A)
TNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSN
CYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTK
SGSTYPVLNVTMPNNDNFDKLYIWGIHHPSTDQEQTSLYVQASGRVTVSTRRSQQTIIPN
IGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDT
CISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGLEVLFQ

Sequence of entity 2 (C), FASTA

>6XPX_2 S1V2-51 Fab light chain (chains C)
DIVMTQSPESLAVSLGERATINCKSSQSVSFGSSDKNYLGWYQQKPGQPPKLLINWASTR
ESGVSDRFRGTGSGTDFTLTISSLQAEDAAVYYCHQYYTPPYSFGQGTKLEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>6XPX_3 S1V2-51 Fab heavy chain (chains B)
QVQLVESGGGVVQPGRSLRLSCVASGFTFRDSVMHWVRQAPGKGLEWVAVTSFDGGESYS
ADSVKGRFTISRDNSKSTLSLQMNILRPEDTGVYYCARDRGGLDVWGQGTTVTVSGASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
BCN	Bicine	C6 H13 N O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (1PE, GOL) are not listed.

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 P03437), best resolution first:

8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
8PJG 1.83 Å, F11 TCR in complex with Human Leukocyte Antigen class II allotype DR1 presenting P11T->R…
1QU1 1.9 Å, Crystal structure of EHA2 (23-185)
6E56 2.0 Å, Human antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2)
1PYW 2.1 Å, Human class II MHC protein HLA-DR1 bound to a designed peptide related to influenza…
3S5L 2.1 Å, Crystal structure of CD4 mutant bound to HLA-DR1
1J8H 2.4 Å, Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA…
3S4S 2.4 Å, Crystal structure of CD4 mutant bound to HLA-DR1
1HTM 2.5 Å, Structure of influenza haemagglutinin at the PH of membrane fusion
2VIU 2.5 Å, Influenza virus hemagglutinin
1FYT 2.6 Å, Crystal structure of a complex of a human alpha/beta-T cell receptor, influenza ha…

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