6VLN: 4498 Fab

Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and anti-Kappa VHH domain. Determined by X-ray diffraction at 1.63 Å resolution. Released 17 Jun 2020.

Method: X-ray diffraction
Resolution: 1.63 Å
Organisms: Homo sapiens, Camelidae mixed library, Plasmodium falciparum
Chains: 4
Atoms: 4,712
Mol. weight: 60.81 kDa
Released: 17 Jun 2020

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

Secondary structure: helices and β-sheets

6VLN contains 22 α-helices and 56 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 H: 11 helices, 24 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
α-helix	61-63	3
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
β-strand	98-99	2	3
β-strand	100E-100F	2	3
β-strand	100J-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
α-helix	128-130	3
β-strand	131-132	2	5
β-strand	135-145	11	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	176-185	10	5
α-helix	186-188	3
β-strand	195-200	6	6
α-helix	201-203	3
β-strand	205-210	6	6

Chain K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	46-51	6	13
β-strand	58-60	3	13
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	108-111	4	13
β-strand	115-119	5	13

Chain L: 8 helices, 21 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	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-198	8	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4498 Fab heavy chain	H	protein	230	Homo sapiens
4498 Fab light chain	L	protein	213	Homo sapiens
anti Kappa VHH domain	K	protein	121	Camelidae mixed library
Circumsporozoite protein	P	protein	12	Plasmodium falciparum	P19597 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6VLN_1 4498 Fab heavy chain (chains H)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSIYGMHWVRQAPGKGLEWVALIWYDGTNKYY
TDSVKGRFTISRDNSKNTLFLQMNSVRAEDTAVYYCARDAHYSDSSGYSSWGYFDYWGQG
SLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6VLN_2 4498 Fab light chain (chains L)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIFDASIRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWYTFGQGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (K), FASTA

>6VLN_3 anti Kappa VHH domain (chains K)
XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXX
XDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVS
S

Sequence of entity 4 (P), FASTA

>6VLN_4 Circumsporozoite protein (chains P)
NVDPNANPNVDP

Primary citation

Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs. Murugan, R., Scally, S.W., Costa, G. et al. Nat Med (2020) 26:1135-1145. DOI 10.1038/s41591-020-0881-9 · PubMed

Other PDB entries of the same protein (UniProt P19597 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O24 1.4 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein NANP3 and…
8FDD 1.54 Å, Crystal structure of Ky15.3 Fab in complex with circumsporozoite protein NPDP peptide
8FAS 1.55 Å, Crystal structure of Ky230 Fab in complex with circumsporozoite protein NANP5 peptide
8FB8 1.69 Å, Crystal structure of Ky15.10-Y100EK Fab in complex with circumsporozoite protein KQPA…
6ULF 1.7 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein NDN3 and…
8F9U 1.7 Å, Crystal structure of Ky15.7 Fab in complex with circumsporozoite protein NPDP peptide
8FB7 1.75 Å, Crystal structure of Ky15.10 Fab in complex with circumsporozoite protein NPDP peptide
6O26 1.8 Å, Crystal structure of 3246 Fab in complex with circumsporozoite protein NANA
8FA7 1.8 Å, Crystal structure of Ky15.11 Fab in complex with circumsporozoite protein KQPA peptide
8FA8 1.8 Å, Crystal structure of Ky15.11 Fab in complex with circumsporozoite protein NDN peptide
8FDC 1.8 Å, Crystal structure of Ky311 Fab in complex with circumsporozoite protein KQPA peptide
8F9T 1.85 Å, Crystal structure of Ky15.2 Fab in complex with circumsporozoite protein NPDP peptide

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