9DSS: Fab 7088

Crystal structure of Fab 7088 in complex with NPNA3 peptide from circumsporozoite protein. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Plasmodium falciparum 3D7
Chains: 3
Atoms: 3,339
Mol. weight: 49.05 kDa
Released: 1 Oct 2025

Explore 9DSS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DSS contains 15 α-helices and 42 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 A: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	8	1	3

Chain B: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-137	9	9
β-strand	147-150	4	10
β-strand	153-154	2	10
β-strand	159-163	5	9
β-strand	174-182	9	9
α-helix	183-187	5
β-strand	191-196	6	10
β-strand	205-210	6	10

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96-97	2
β-strand	100B	1	3
β-strand	100F-103	4	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	4
α-helix	118-119	2
β-strand	120-124	5	5
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-184	9	5
α-helix	186-190	5
β-strand	194-200	7	6
α-helix	201-203	3
β-strand	205-211	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of Fab 7088	C	protein	227	Homo sapiens
Light Chain of Fab 7088	B	protein	215	Homo sapiens
Circumsporozoite protein	A	protein	12	Plasmodium falciparum 3D7	Q7K740 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9DSS_1 Heavy chain of Fab 7088 (chains C)
QVQLVESGGGVVQPGRSLRLSCAASGFAFNTYGMHWVRQTPGKGLEWVAIIWYDGSQKYY
ADSVQGRFIISRDNHKNTLSLQMNGLRAEDTAVYFCVRVRFSVGPHGSAFDLWGQGTMVI
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 2 (B), FASTA

>9DSS_2 Light Chain of Fab 7088 (chains B)
GVQMTQSPSTLSASVGDRVTLTCRASQSISSWLAWYQQKPGKAPKLLIYDASSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYSFWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>9DSS_3 Circumsporozoite protein (chains A)
NPNANPNANPNA

Primary citation

Engineered antibodies preserve structural and functional recognition of Plasmodium falciparum circumsporozoite protein. Jain, M., Agrawal, S., Cannac, F. et al. Protein Sci (2026) 35:e70738-e70738. DOI 10.1002/pro.70738 · PubMed

Other PDB entries of the same protein (UniProt Q7K740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SG5 1.4 Å, Structure of PfCSP peptide 21 with antibody CIS43_Var2
9C79 1.46 Å, Human monoclonal antibody MAD21-101 bound to the N-terminus of cleaved circumsporozoite…
9NKZ 1.48 Å, Crystal structure of Fab MAM01 in complex with NANP6 peptide from circumsporozoite protein
9NL0 1.54 Å, Crystal structure of Fab MAM01 in complex with NPNA3 peptide from circumsporozoite protein
7SG6 1.55 Å, Structure of PfCSP peptide 21 with antibody CIS43_Var10
6PBV 1.57 Å, Crystal structure of Fab668 complex
9NCY 1.63 Å, Fab1392 in complex with the C-terminal alpha-TSR domain of the P. falciparum…
3VDJ 1.7 Å, Crystal structure of circumsporozoite protein aTSR domain, R32 native form
9DST 1.74 Å, Crystal structure of Fab MS-1805 in complex with N-terminal junction peptide from…
9NI1 1.75 Å, Fab389 in complex with the C-terminal alpha-TSR domain of the P. falciparum…
7RXP 1.76 Å, Fab1512 in complex with the C-terminal alpha-TSR domain of P. falciparum
6BQB 1.77 Å, MGG4 Fab in complex with peptide

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