5W6G: Human antibody 6649

Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands. Determined by X-ray diffraction at 2.79 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 2.79 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Homo sapiens
Chains: 4
Atoms: 7,347
Mol. weight: 107.36 kDa
Ligands: NAG
Released: 20 Dec 2017

Explore 5W6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W6G contains 27 α-helices and 97 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: 7 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	12	1	2
β-strand	19-20	2	3
β-strand	28-29	2	3
β-strand	30	1	4
β-strand	33-35	3	5
β-strand	37-38	2	6
β-strand	41	1	7
β-strand	45-48	4	8
β-strand	51	1	8
β-strand	54-55	2	9
β-strand	59	1	10
α-helix	61-66	6
β-strand	80	1	11
β-strand	83-85	3	9
β-strand	91	1	10
β-strand	99	1	11
α-helix	102-108	7
β-strand	112-118	7	11
α-helix	123-126	4
β-strand	131	1	12
β-strand	136-141	6	13
β-strand	144-146	3	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	157	1	14
β-strand	160	1	14
β-strand	164-169	6	15
β-strand	175-184	10	11
α-helix	188-195	8
β-strand	202-205	4	15
β-strand	210-213	4	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
α-helix	238	1
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	257-262	6	11
β-strand	268-270	3	9
α-helix	273-274	2
β-strand	275-280	6	8
β-strand	282-284	3	17
β-strand	287-288	2	17
β-strand	289	1	7
β-strand	295-296	2	6
β-strand	303-304	2	17
α-helix	307	1
β-strand	308-309	2	6
β-strand	316-318	3	5
β-strand	322	1	4

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	506	1	18
β-strand	510	1	18
β-strand	514	1	2
β-strand	522-527	6	1
β-strand	532-536	5	1
α-helix	538-557	20
β-strand	564-565	2	17
α-helix	575-625	51
β-strand	630-632	3	1
β-strand	637-640	4	1
α-helix	646-653	8
α-helix	660-662	3
α-helix	663-671	9

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-25	8	19
β-strand	34-41	8	20
β-strand	48-53	6	20
β-strand	59-61	3	20
α-helix	63-65	3
β-strand	69-74	6	19
β-strand	79-84	6	19
α-helix	89-91	3
β-strand	93-101	9	20
α-helix	105-107	3
β-strand	113	1	20
β-strand	119-123	5	20
β-strand	129	1	21
β-strand	132-136	5	22
α-helix	137-139	3
β-strand	147-157	11	22
β-strand	158	1	21
β-strand	163-166	4	23
α-helix	167-169	3
β-strand	171	1	23
β-strand	175-177	3	22
α-helix	178-180	3
β-strand	181-182	2	22
β-strand	188-197	10	22
β-strand	207-211	5	23
α-helix	213-215	3
β-strand	218-222	5	23

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	24
β-strand	5	1	25
β-strand	9-12	4	26
β-strand	18-23	6	25
α-helix	29-31	3
β-strand	36-40	5	26
β-strand	47-50	4	26
β-strand	51	1	27
β-strand	55	1	27
β-strand	64-69	6	25
β-strand	72-77	6	25
α-helix	82-84	3
β-strand	87-94	8	26
β-strand	100-103	4	26
β-strand	104	1	24
β-strand	107-111	5	26
α-helix	117-119	3
β-strand	120-124	5	28
α-helix	125-127	3
α-helix	128-131	4
β-strand	136-145	10	28
β-strand	151-156	6	29
β-strand	159-161	3	29
β-strand	165-167	3	28
α-helix	168-170	3
β-strand	171-172	2	28
β-strand	178-186	9	28
α-helix	188-193	6
β-strand	197-203	7	29
β-strand	206-212	7	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A	protein	334	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7UPX0
Hemagglutinin HA2	B	protein	178	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7UPX0
6649 antibody heavy chain	H	protein	230	Homo sapiens	S6B2B6 (AlphaFold model)
6649 antibody light chain	L	protein	218	Homo sapiens	Q6GMX4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5W6G_1 Hemagglutinin HA1 (chains A)
ADPGYLLEDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQL
GNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFE
RFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEV
LVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTL
LEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQ
NVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>5W6G_2 Hemagglutinin HA2 (chains B)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDGVRS

Sequence of entity 3 (H), FASTA

>5W6G_3 6649 antibody heavy chain (chains H)
QVQLQESGPGLVKTSETLSLTCTVSGGSIKNKDFFWAWIRQPPGKALEWIGSVFYSGGAY
YNWSLRNRVTMSADTSKNQFSLKMTSVTASDTSFYYCATSYVDNWHAGLHWFDSWGRGTL
VTVSGASTKGPSVFPLAPSSKSTSGGTVALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 4 (L), FASTA

>5W6G_4 6649 antibody light chain (chains L)
QSVLTQPPSVSGAPGQRVSISCTGTHSNIGAGFDVHWYQQLPGTAPKLLIYANNNRPSGV
PDRFSGSKSGSSASLAITGLQAEDEADYYCQSFDSILSGDLVFGGGTKLTVLGQPKGAPS
VTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAA
SSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody. Raymond, D.D., Bajic, G., Ferdman, J. et al. Proc Natl Acad Sci U S A (2018) 115:168-173. DOI 10.1073/pnas.1715471115 · PubMed

Other PDB entries of the same protein (UniProt A7UPX0), best resolution first:

5W0D 1.9 Å, Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza…
4HKX 2.5 Å, Influenza hemagglutinin in complex with CH67 Fab
4YJZ 2.72 Å, Human antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
4YK4 2.8 Å, Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
9E6J 2.98 Å, DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
6Q0O 3.0 Å, human antibody H2227 lineage 652 in complex with influenza hemagglutinin head domain of…
5UG0 3.4 Å, Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin
5UJZ 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK0 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK1 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK2 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…

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