6WFZ: Fab399

Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein. Determined by X-ray diffraction at 1.84 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.84 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 6
Atoms: 7,168
Mol. weight: 98.39 kDa
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6WFZ contains 41 α-helices and 96 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: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	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	46-51	6	3
α-helix	52B-53	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	68-72	5	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	3
α-helix	96	1
β-strand	100B-103	4	3
β-strand	107-109	3	3
β-strand	110-111	2	2
α-helix	115-116	2
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
α-helix	186-188	3
β-strand	189	1	7
β-strand	192	1	7
β-strand	194-200	7	6
α-helix	201-203	3
β-strand	205-211	7	6

Chain B: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	27C	1	10
β-strand	31	1	10
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
α-helix	96	1
β-strand	97-98	2	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	129-139	11	12
β-strand	140	1	11
β-strand	145-150	6	13
β-strand	153-154	2	13
β-strand	159-163	5	12
α-helix	164-167	4
β-strand	173-182	10	12
α-helix	183-186	4
β-strand	191-197	7	13
β-strand	205-210	6	13

Chains C and P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain H: 11 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
α-helix	52B-53	3
β-strand	57-59	3	16
α-helix	61-63	3
β-strand	67-72	6	14
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-95	8	16
α-helix	96	1
β-strand	100B-103	4	16
β-strand	107-109	3	16
β-strand	110-111	2	15
α-helix	115-116	2
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
α-helix	155-157	3
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
α-helix	186-188	3
β-strand	189	1	20
β-strand	192	1	20
β-strand	195-200	6	19
α-helix	201-203	3
β-strand	205-210	6	19

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	27C	1	23
β-strand	31	1	23
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	84-90	7	22
α-helix	96	1
β-strand	97-98	2	22
β-strand	102-106	5	22
β-strand	111	1	24
α-helix	112-113	2
β-strand	114-118	5	25
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	25
β-strand	140	1	24
β-strand	145-150	6	26
β-strand	153-154	2	26
α-helix	155	1
β-strand	159-163	5	25
α-helix	164-167	4
β-strand	173-182	10	25
α-helix	183-186	4
β-strand	191-197	7	26
β-strand	205-210	6	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab399 heavy chain	A, H	protein	224	Homo sapiens
Fab399 light chain	B, L	protein	219	Homo sapiens
NPNA3 peptide	C, P	protein	14	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>6WFZ_1 Fab399 heavy chain (chains A, H)
EVQLVESGGGLVQPGRSLRLSCTTSGFTFGDYAMSWFRQAPGKGLEWVGFIRSKGFGGTA
EYAAFVKGRFTISRDDSRSIAYLQMTSLKPEDTAVYYCSRVGVVIATAVYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, L), FASTA

>6WFZ_2 Fab399 light chain (chains B, L)
DILMTQTPLSLSVTPGQPASISCKSSQSLLDNDGKTYLYWYLQKPGQSPQLLIYEVSNRF
SGVPERFSGSGSGTDFTLKIRRVEAEDVGVYYCMQRIDLPWTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, P), FASTA

>6WFZ_3 NPNA3 peptide (chains C, P)
XNPNANPNANPNAX

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:

6WFY 1.23 Å, Crystal structure of Fab224 in complex with NPNA4 peptide from circumsporozoite protein
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…
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…

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