6D0X: Chimeric H.2140 / K.1210 Fab

Crystal structure of chimeric H.2140 / K.1210 Fab in complex with circumsporozoite protein NANP3. Determined by X-ray diffraction at 1.85 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, Plasmodium falciparum
Chains: 3
Atoms: 3,655
Mol. weight: 49.26 kDa
Released: 13 Jun 2018

Explore 6D0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D0X contains 18 α-helices and 43 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 A: 11 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
α-helix	73-75	3
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100G-103	4	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	125-127	3
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	188-191	4
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-197	7	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2140 Antibody, heavy chain	A	protein	227	Homo sapiens
1210 Antibody, light chain	B	protein	213	Homo sapiens
NANP3	C	protein	12	Plasmodium falciparum	P02893 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6D0X_1 2140 Antibody, heavy chain (chains A)
QVQLVESGGGVVQPGTSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAIIWYDGSKKYY
ADSVKGRFTISRDNSRNTLYLQMNSLRAEDTAVYYCAKVGEGQVGDSSGYYDHWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (B), FASTA

>6D0X_2 1210 Antibody, light chain (chains B)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASNLESGVPL
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYNNYWTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>6D0X_3 NANP3 (chains C)
NANPNANPNANP

Primary citation

Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope. Imkeller, K., Scally, S.W., Bosch, A. et al. Science (2018) 360:1358-1362. DOI 10.1126/science.aar5304 · 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…
6WFZ 1.84 Å, Crystal structure of Fab399 in complex with NPNA3 peptide from circumsporozoite protein
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

About this viewer

MolViewer shows 6D0X 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.