6O29: 4493 Fab

Crystal structure of 4493 Fab in complex with circumsporozoite protein NPDP and anti-kappa VHH domain. Determined by X-ray diffraction at 2.4 Å resolution. Released 1 Jul 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Plasmodium falciparum, Lama glama
Chains: 8
Atoms: 8,344
Mol. weight: 120.67 kDa
Released: 1 Jul 2020

Explore 6O29 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O29 contains 39 α-helices and 112 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.

Chain A: 8 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
α-helix	52B-53	3
β-strand	57-58	2	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96-97	2
β-strand	100C-103	4	2
β-strand	107-111	5	2
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
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	186-189	4
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

Chain B: 9 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
α-helix	30-32	3
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
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
α-helix	155	1
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

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	24
β-strand	11-12	2	25
β-strand	18-25	8	24
β-strand	33-39	7	26
β-strand	46-51	6	26
β-strand	57-59	3	26
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	84-86	3
β-strand	88-95	8	26
β-strand	100D-103	4	26
β-strand	104	1	24
β-strand	107-109	3	26
β-strand	110-111	2	25

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
α-helix	52B-53	3
β-strand	57-58	2	12
β-strand	67-72	6	11
β-strand	77-82	6	11
α-helix	84-86	3
β-strand	88-95	8	12
α-helix	96-97	2
β-strand	100C-103	4	12
β-strand	107-111	5	12
β-strand	117	1	13
α-helix	118-119	2
β-strand	120-124	5	14
β-strand	131	1	14
β-strand	135-145	11	14
β-strand	146	1	13
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	159	1	15
β-strand	163-165	3	14
α-helix	166-168	3
β-strand	169-170	2	14
β-strand	176-185	10	14
α-helix	186-189	4
β-strand	194-200	7	15
α-helix	201-203	3
β-strand	205-211	7	15

Chain K: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
β-strand	18-25	8	21
β-strand	33-39	7	23
β-strand	46-51	6	23
β-strand	57-59	3	23
α-helix	61-63	3
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-95	8	23
β-strand	100D-103	4	23
β-strand	104	1	21
β-strand	107-109	3	23
β-strand	110-111	2	22

Chain L: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-28	11	16
α-helix	30-32	3
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
β-strand	62-75	14	16
α-helix	80-82	3
β-strand	85-90	6	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-106	5	17
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
α-helix	155	1
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	191-197	7	20
β-strand	205-210	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4493 Fab heavy chain	A, H	protein	225	Homo sapiens
4493 Kappa light chain	B, L	protein	215	Homo sapiens
Circumsporozoite protein	C, D	protein	16	Plasmodium falciparum	P19597 (AlphaFold model)
Anti-kappa VHH domain	E, K	protein	121	Lama glama

Sequence of entity 1 (A, H), FASTA

>6O29_1 4493 Fab heavy chain (chains A, H)
EVQLVESGGGLVQPGRSLRLSCTASGFTFGDYAMSWVRQAPGKGLEWVGFIRSKANGGRT
ENPASVKGRFTISRDDSKSIAYLQMNSLKTEDTAVYYCTRVELGSSWSLGYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, L), FASTA

>6O29_2 4493 Kappa light chain (chains B, L)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSTYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, D), FASTA

>6O29_3 Circumsporozoite protein (chains C, D)
NPDPNANPNVDPNANP

Sequence of entity 4 (E, K), FASTA

>6O29_4 Anti-kappa VHH domain (chains E, K)
XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXX
XDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVS
S

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
6VLN 1.63 Å, Crystal structure of 4498 Fab in complex with circumsporozoite protein DND3 and…
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

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