6PBW: Fab667 complex

Crystal structure of Fab667 complex. Determined by X-ray diffraction at 2.06 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Homo sapiens, Plasmodium falciparum 3D7
Chains: 3
Atoms: 3,501
Mol. weight: 49.33 kDa
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6PBW contains 15 α-helices and 47 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 C: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-13	4	3
β-strand	19-24	6	2
β-strand	33-38	6	3
β-strand	45-48	4	3
β-strand	49	1	4
β-strand	53	1	4
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	84-91	8	3
β-strand	96-98	3	3
β-strand	99	1	1
β-strand	102-106	5	3
α-helix	108-110	3
β-strand	111	1	5
α-helix	112-113	2
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	6
β-strand	140	1	5
β-strand	145-150	6	7
β-strand	153-155	3	7
β-strand	159-161	3	6
α-helix	162-164	3
β-strand	165-166	2	6
β-strand	172-180	9	6
α-helix	182-187	6
β-strand	191-197	7	7
β-strand	200-206	7	7

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	32-39	8	9
β-strand	45-52	8	9
β-strand	57-59	3	9
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	102-103	2	9
β-strand	107-111	5	9
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	194-200	7	12
α-helix	201-203	3
β-strand	205-211	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab667 light chain	C	protein	216	Homo sapiens
Fab667 heavy chain	D	protein	231	Homo sapiens
NPNANPNANPNA peptide	E	protein	14	Plasmodium falciparum 3D7	Q7K740 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6PBW_1 Fab667 light chain (chains C)
QSALTQPDSVSGSPGQSITISCTGTSNDVGIYNHVSWYQQHPGKAPKLMIYDVNKRPSGI
SNRFSGSKSGDTASLTISGLQAEDEADYYCCSYAGSSAWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (D), FASTA

>6PBW_2 Fab667 heavy chain (chains D)
QVQLVQSGAEVKKPGASVKVSCRASGYTFTNYAMHWVRQAPGQRLEWMGWINAGNGYTKY
SQKFQDRVTITRDTSATTAYMELSSLRSEDTAMYYCARDSFYDILSGPVYHYYGMDVWGQ
GTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (E), FASTA

>6PBW_3 NPNANPNANPNA peptide (chains E)
XNPNANPNANPNAX

Primary citation

Structure and mechanism of monoclonal antibody binding to the junctional epitope of Plasmodium falciparum circumsporozoite protein. Oyen, D., Torres, J.L., Aoto, P.C. et al. PLoS Pathog (2020) 16:e1008373-e1008373. DOI 10.1371/journal.ppat.1008373 · 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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