7LKB: M42.127 Fab heavy Chain

Crystal structure of PfCSP peptide 21 with vaccine-elicited human anti-malaria antibody m42.127. Determined by X-ray diffraction at 1.8 Å resolution. Released 15 Dec 2021.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Homo sapiens, Plasmodium falciparum 3D7
Chains: 6
Atoms: 7,618
Mol. weight: 102.24 kDa
Released: 15 Dec 2021

Explore 7LKB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LKB contains 37 α-helices and 94 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.

Chains A and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	10	1	2

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-52	8	13
β-strand	57-59	3	13
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-98	11	13
β-strand	100C-103	5	13
β-strand	107-111	5	13
α-helix	115-116	2
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-124	5	15
α-helix	128-130	3
β-strand	131-132	2	15
β-strand	135-145	11	15
β-strand	146	1	14
β-strand	151-154	4	16
α-helix	155-157	3
β-strand	159	1	16
β-strand	164-165	2	15
α-helix	166-168	3
β-strand	169-170	2	15
β-strand	176-185	10	15
α-helix	186-190	5
β-strand	195-200	6	16
α-helix	201-203	3
β-strand	205-210	6	16

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	27C-27D	2	19
β-strand	30-31	2	19
β-strand	33-38	6	18
β-strand	45-49	5	18
β-strand	53-54	2	18
α-helix	55	1
β-strand	62-67	6	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	84-90	7	18
α-helix	96	1
β-strand	97-98	2	18
β-strand	102-107	6	18
β-strand	114	1	20
α-helix	115-116	2
β-strand	117-121	5	21
α-helix	122-124	3
α-helix	125-129	5
β-strand	132-142	11	21
β-strand	143	1	20
β-strand	147-153	7	22
β-strand	156-157	2	22
α-helix	158	1
β-strand	162-166	5	21
α-helix	167-170	4
β-strand	176-185	10	21
α-helix	186-190	5
β-strand	194-201	8	22
β-strand	208-213	6	22

Chain H: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-52	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	88-98	11	2
β-strand	100C-103	5	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	128-130	3
β-strand	131-132	2	4
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	186-188	3
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-14	5	7
β-strand	19-25	7	6
β-strand	27C-27D	2	8
β-strand	30-31	2	8
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
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-107	6	7
β-strand	114	1	9
α-helix	115-116	2
β-strand	117-121	5	10
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	10
β-strand	143	1	9
β-strand	147-153	7	11
β-strand	156-157	2	11
β-strand	162-166	5	10
α-helix	167-170	4
β-strand	176-185	10	10
α-helix	186-189	4
β-strand	194-201	8	11
β-strand	208-213	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
m42.127 Fab heavy Chain	B, H	protein	233	Homo sapiens
m42.127 Fab light chain	C, L	protein	223	Homo sapiens
Circumsporozoite protein	A, D	protein	15	Plasmodium falciparum 3D7	Q7K740 (AlphaFold model)

Sequence of entity 1 (B, H), FASTA

>7LKB_1 m42.127 Fab heavy Chain (chains B, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYAIHWVRQAPGQRLEWMGWIKAGNGNTRY
SQKFQDRVTITRDTSASTAYMELSSLRSEDTAVYYCALLTVITPDDTFDIWGQGTMVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 2 (C, L), FASTA

>7LKB_2 m42.127 Fab light chain (chains C, L)
DIVMTQSPDSLAVSLGERATINCKSSQNILYSSNNKNYLAWYQQKPGQAPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCHQYYSSPLTFGGGTKVEIKRADRTVA
APSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDS
TYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, D), FASTA

>7LKB_3 Circumsporozoite protein (chains A, D)
NPDPNANPNVDPNAN

Primary citation

Vaccination in a humanized mouse model elicits highly protective PfCSP-targeting anti-malarial antibodies. Kratochvil, S., Shen, C.H., Lin, Y.C. et al. Immunity (2021) 54:2859-2876.e7. DOI 10.1016/j.immuni.2021.10.017 · 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

Browse structure collections

About this viewer

MolViewer shows 7LKB 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.