6WFY: Fab224

Crystal structure of Fab224 in complex with NPNA4 peptide from circumsporozoite protein. Determined by X-ray diffraction at 1.23 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.23 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 3
Atoms: 3,930
Mol. weight: 49.16 kDa
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6WFY contains 19 α-helices and 49 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 H: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-51	7	3
α-helix	52B-53	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
α-helix	96	1
β-strand	99	1	4
β-strand	100D	1	4
β-strand	100H-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	5
α-helix	118-119	2
β-strand	120-124	5	6
α-helix	128-130	3
β-strand	131-132	2	6
β-strand	135-145	11	6
β-strand	146	1	5
β-strand	151-154	4	7
α-helix	155-157	3
β-strand	159	1	7
β-strand	163-165	3	6
α-helix	166-168	3
β-strand	169-170	2	6
β-strand	176-185	10	6
α-helix	186-188	3
β-strand	195-200	6	7
α-helix	201-203	3
β-strand	205-210	6	7

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	9-13	4	9
β-strand	19-24	6	8
α-helix	27C-29	3
β-strand	34-38	5	9
β-strand	45-48	4	9
β-strand	49	1	10
β-strand	53	1	10
α-helix	54-55	2
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-92	9	9
β-strand	95B-98	4	9
β-strand	102-106	5	9
β-strand	111	1	11
α-helix	112-113	2
β-strand	114-118	5	12
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-155	3	13
β-strand	159-161	3	12
α-helix	162-164	3
β-strand	165-166	2	12
β-strand	172-180	9	12
α-helix	182-186	5
β-strand	191-197	7	13
β-strand	200-206	7	13

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab224 heavy chain	H	protein	230	Homo sapiens
Fab224 light chain	L	protein	217	Homo sapiens
NPNA4 peptide	P	protein	18	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6WFY_1 Fab224 heavy chain (chains H)
EVQLVESGGGLVQPGRSLRLPCTASGFSFGDHAMSWVRQAPGKGLEWVGFIRKTTYGATT
HYAAAVRGRFTISRDDSKSIVYLQMNSLKTEDTAVYFCTRVQLDYGPGYQYYGMDVWGQG
TTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6WFY_2 Fab224 light chain (chains L)
ESVLTQPPSVSGAPGQRVTISCTGMNSNIGAGYDVYWYQQLPGRAPKLLIYGNSNRPSGV
PDRFSGSRSGTSASLAITGLQAEDEADYYCQSYDTSLNGWAFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLVSDFYPGAVTVAWKADGSPVKVGVETTKPSKQSNNKYAAS
SYLSLTPEQWKSHRSYSCRVTHEGSTVEKTVAPAECS

Sequence of entity 3 (P), FASTA

>6WFY_3 NPNA4 peptide (chains P)
XNPNANPNANPNANPNAX

Primary citation

Structural and biophysical correlation of anti-NANP antibodies with in vivo protection against P. falciparum. Pholcharee, T., Oyen, D., Flores-Garcia, Y. et al. Nat Commun (2021) 12:1063-1063. DOI 10.1038/s41467-021-21221-4 · PubMed

Other PDB entries of the same protein (UniProt P02893 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WG0 1.6 Å, Crystal structure of Fab366 in complex with NPNA3 peptide from circumsporozoite protein
6AZM 1.6 Å, Crystal structure of the 580 germline antibody bound to circumsporozoite protein NANP…
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
7RD4 1.75 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
6B5R 1.77 Å, Structure of PfCSP peptide 21 with human antibody CIS42
6B5M 1.79 Å, Structure of PfCSP peptide 21 with human protective antibody CIS43
7RD3 1.81 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…
6WFZ 1.84 Å, Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein
6D0X 1.85 Å, Crystal structure of chimeric H.2140 / K.1210 Fab in complex with circumsporozoite…
6UUD 1.85 Å, Crystal structure of antibody 5D5 in complex with PfCSP N-terminal peptide
6W00 1.85 Å, Crystal structure of Fab239 in complex with NPNA2 peptide from circumsporozoite protein
7RD9 1.91 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…

Browse structure collections

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