4YK4: Human antibody 641 I-9

Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006. Determined by X-ray diffraction at 2.8 Å resolution. Released 27 May 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 6
Atoms: 10,127
Mol. weight: 151.15 kDa
Ligands: NAG
Released: 27 May 2015

Explore 4YK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YK4 contains 40 α-helices and 132 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	59	1	31
α-helix	61-66	6
β-strand	91	1	31
β-strand	99	1	32
α-helix	102-108	7
β-strand	116-119	4	32
β-strand	131	1	33
β-strand	136-140	5	34
β-strand	145-146	2	34
β-strand	151-153	3	32
β-strand	155	1	33
β-strand	157	1	35
β-strand	160	1	35
α-helix	162-163	2
β-strand	164-169	6	36
β-strand	176-184	9	32
α-helix	188-195	8
β-strand	202-205	4	36
β-strand	210-213	4	36
β-strand	223	1	37
β-strand	226	1	37
β-strand	229-237	9	32
α-helix	238	1
β-strand	242-247	6	36
β-strand	251-254	4	32
β-strand	256-259	4	32

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-14	5	21
β-strand	19-25	7	20
β-strand	33-38	6	21
β-strand	45-49	5	21
β-strand	53-54	2	21
α-helix	55	1
β-strand	62-67	6	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	84-90	7	21
β-strand	98	1	21
β-strand	102-107	6	21
β-strand	111	1	22
α-helix	112-113	2
β-strand	114-118	5	23
α-helix	122-125	4
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	144-150	7	24
β-strand	153-154	2	24
α-helix	155	1
β-strand	159-163	5	23
α-helix	164-167	4
β-strand	173-182	10	23
α-helix	183-188	6
β-strand	191-198	8	24
β-strand	205-210	6	24

Chain C: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	11-12	2	26
β-strand	18-25	8	25
β-strand	33-39	7	27
β-strand	46-52	7	27
β-strand	57-59	3	27
β-strand	67-72	6	25
α-helix	73-75	3
β-strand	77-82	6	25
α-helix	87-89	3
β-strand	91-104	14	27
β-strand	107-115	9	27
β-strand	119-121	3	27
β-strand	122-123	2	26
α-helix	127-128	2
β-strand	129	1	28
α-helix	130-131	2
β-strand	132-136	5	29
β-strand	148-157	10	29
β-strand	158	1	28
β-strand	163-166	4	30
α-helix	167-169	3
β-strand	171	1	30
β-strand	175-177	3	29
α-helix	178-180	3
β-strand	181-182	2	29
β-strand	188-196	9	29
α-helix	200-203	4
β-strand	207-212	6	30
α-helix	213-215	3
β-strand	217-222	6	30

Chain E: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	59	1	13
α-helix	61-66	6
β-strand	91	1	13
β-strand	99	1	14
α-helix	102-108	7
β-strand	116-119	4	14
α-helix	123-126	4
β-strand	131	1	15
β-strand	136-140	5	16
β-strand	145-146	2	16
β-strand	151-153	3	14
β-strand	155	1	15
β-strand	157	1	17
β-strand	160	1	17
α-helix	162-163	2
β-strand	164-169	6	18
β-strand	176-184	9	14
α-helix	188-195	8
β-strand	202-205	4	18
β-strand	210-213	4	18
β-strand	223	1	19
β-strand	226	1	19
β-strand	229-237	9	14
β-strand	242-247	6	18
β-strand	251-254	4	14
β-strand	256-259	4	14

Chain Y: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	98	1	2
β-strand	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain Z: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
β-strand	33-39	7	8
β-strand	46-52	7	8
β-strand	57-59	3	8
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-102	12	8
β-strand	108-115	8	8
β-strand	119-121	3	8
β-strand	122-123	2	7
α-helix	127-128	2
β-strand	129	1	9
α-helix	130-131	2
β-strand	132-136	5	10
β-strand	148-157	10	10
β-strand	158	1	9
β-strand	163-166	4	11
α-helix	167-169	3
β-strand	171	1	11
β-strand	175-177	3	10
α-helix	178-180	3
β-strand	181-182	2	10
β-strand	188-196	9	10
α-helix	198-200	3
β-strand	201	1	12
β-strand	204	1	12
β-strand	207-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
641 I-9 VLCL antibody	B, Y	protein	214	Homo sapiens
641 I-9 VHCH antibody	C, Z	protein	236	Homo sapiens
Hemagglutinin	A, E	protein	230	Influenza A virus	A7UPX0

Sequence of entity 1 (B, Y), FASTA

>4YK4_1 641 I-9 VLCL antibody (chains B, Y)
DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSIPLTFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (C, Z), FASTA

>4YK4_2 641 I-9 VHCH antibody (chains C, Z)
QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTDYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARRRSDFETVDFIYHYMDVWGKGTT
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH

Sequence of entity 3 (A, E), FASTA

>4YK4_3 Hemagglutinin (chains A, E)
ADPGYLLEAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYE
ELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPN
LSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKV
RDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Viral receptor-binding site antibodies with diverse germline origins. Schmidt, A.G., Therkelsen, M.D., Stewart, S. et al. Cell (2015) 161:1026-1034. DOI 10.1016/j.cell.2015.04.028 · 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
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
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…

Browse structure collections

About this viewer

MolViewer shows 4YK4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.