6PBV: Fab668 complex

Crystal structure of Fab668 complex. Determined by X-ray diffraction at 1.57 Å resolution. Released 4 Mar 2020.

Method: X-ray diffraction
Resolution: 1.57 Å
Organisms: Homo sapiens, Plasmodium falciparum 3D7
Chains: 6
Atoms: 7,525
Mol. weight: 97.71 kDa
Released: 4 Mar 2020

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

Secondary structure: helices and β-sheets

6PBV contains 35 α-helices and 94 β-strands across 4 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: 8 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
α-helix	54-55	2
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 B: 10 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
α-helix	61-63	3
β-strand	67-72	6	8
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
α-helix	114-116	3
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
α-helix	171	1
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

Chain C: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	13
β-strand	5	1	14
β-strand	9-13	4	15
β-strand	19-24	6	14
β-strand	33-38	6	15
β-strand	45-48	4	15
β-strand	49	1	16
β-strand	53	1	16
α-helix	54-55	2
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-91	8	15
β-strand	96-98	3	15
β-strand	99	1	13
β-strand	102-106	5	15
α-helix	108-110	3
β-strand	111	1	17
α-helix	112-113	2
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-154	2	19
β-strand	159-161	3	18
α-helix	162-164	3
β-strand	165-166	2	18
β-strand	172-180	9	18
α-helix	182-187	6
β-strand	191-197	7	19
β-strand	200-206	7	19

Chain D: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	10-12	3	21
β-strand	18-25	8	20
α-helix	29-31	3
β-strand	32-39	8	21
β-strand	45-52	8	21
β-strand	57-59	3	21
α-helix	61-63	3
β-strand	67-72	6	20
β-strand	77-82	6	20
α-helix	84-86	3
β-strand	88-96	9	21
β-strand	102-103	2	21
β-strand	107-111	5	21
α-helix	114-116	3
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	176-185	10	23
α-helix	186-188	3
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab668 light chain	A, C	protein	216	Homo sapiens
Fab668 heavy chain	B, D	protein	229	Homo sapiens
Junctional peptide	G, I	protein	16	Plasmodium falciparum 3D7	Q7K740 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6PBV_1 Fab668 light chain (chains A, C)
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNYVSWYQQHPGKAPKLMIYDVNTRPSGV
SIRFSASKSGNTASLTVSGLQAEDEAVYYCSSYAGSSTWVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B, D), FASTA

>6PBV_2 Fab668 heavy chain (chains B, D)
QVQLVQSGAEVKKPGASVKVSCKASGFTFTDYAMHWVRQAPGQRLEWMGWINAGNGYTKY
SQKFQDRLTITRDTFASTVYMELSSLRSEDTTVYYCARDGFCPSNTCSGYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (G, I), FASTA

>6PBV_3 Junctional peptide (chains G, I)
XKQPADGNPDPNANPX

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
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
7LKB 1.8 Å, Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody…

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