5WKZ: VH1-69 germline antibody predicted from CR6261

VH1-69 germline antibody predicted from CR6261. Determined by X-ray diffraction at 1.85 Å resolution. Released 1 Aug 2018.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,559
Mol. weight: 49.6 kDa
Released: 1 Aug 2018

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

Secondary structure: helices and β-sheets

5WKZ contains 18 α-helices and 48 β-strands across 2 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 H: 11 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	6	2
β-strand	45-52	8	2
α-helix	53-55	3
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	108-111	4	2
β-strand	115-119	5	2
α-helix	122-124	3
β-strand	125	1	3
α-helix	126-127	2
β-strand	128-132	5	4
α-helix	136-138	3
β-strand	139-140	2	4
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	159-162	4	5
α-helix	163-165	3
β-strand	167	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
β-strand	184-193	10	4
α-helix	194-196	3
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	6
β-strand	3	1	7
β-strand	7-10	4	8
β-strand	16-21	6	7
α-helix	27-29	3
β-strand	33-37	5	8
β-strand	44-47	4	8
β-strand	48	1	9
β-strand	52	1	9
β-strand	61-66	6	7
β-strand	69-74	6	7
α-helix	79-81	3
β-strand	83-91	9	8
β-strand	97-100	4	8
β-strand	101	1	6
β-strand	104-108	5	8
β-strand	114	1	10
α-helix	115-116	2
β-strand	117-121	5	11
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	11
β-strand	143	1	10
β-strand	148-153	6	12
β-strand	156-158	3	12
β-strand	162-164	3	11
α-helix	165-167	3
β-strand	168-169	2	11
β-strand	175-183	9	11
α-helix	185-190	6
β-strand	194-200	7	12
β-strand	203-209	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Immunoglobulin heavy variable 1-69D,IgG H chain	H	protein	250	Homo sapiens	A0A0B4J2H0 (AlphaFold model), S6BAM6 (AlphaFold model)
Lambda-chain (AA -20 to 215)	L	protein	217	Homo sapiens	A2NUT2 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>5WKZ_1 Immunoglobulin heavy variable 1-69D,IgG H chain (chains H)
QVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTANY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARHMGYQLRETMDVWGKGTTVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCGSGGGLNDIFEAQKIE
WHECHHHHHH

Sequence of entity 2 (L), FASTA

>5WKZ_2 Lambda-chain (AA -20 to 215) (chains L)
QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAYVVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Anti-idiotypic antibody K1-18 engages VH1-69 precursor and affinity-matured, anti-stem antibodies through mimicry of the HA stem. Wilson, I.A., Lang, S., Kurosawa, Y. et al. To be published.

Other PDB entries of the same protein (UniProt A0A0B4J2H0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C2B 1.4 Å, anti-CXCL13 parental scFv - 3B4
5C6W 1.54 Å, anti-CXCL13 scFv - E10
5CBE 2.4 Å, E10 in complex with CXCL13
5CBA 2.5 Å, 3B4 in complex with CXCL13 - 3B4-CXCL13

Browse structure collections

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