6O25: 3945 Fab

Crystal structure of 3945 Fab in complex with circumsporozoite protein NANP3 and anti-Kappa VHH domain. Determined by X-ray diffraction at 2.9 Å resolution. Released 1 Jul 2020.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Lama glama, Plasmodium falciparum
Chains: 12
Atoms: 12,136
Mol. weight: 180.05 kDa
Released: 1 Jul 2020

Explore 6O25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O25 contains 57 α-helices and 177 β-strands across 11 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: 7 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
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	88-95	8	2
α-helix	96	1
β-strand	100D-102	3	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
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	194-200	7	5
β-strand	205-211	7	5

Chain B: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	18
β-strand	10-13	4	19
β-strand	19-25	7	18
α-helix	27A-28	2
α-helix	29-31	3
β-strand	33-38	6	19
β-strand	45-49	5	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	85-90	6	19
β-strand	97-98	2	19
β-strand	102-106	5	19
β-strand	110	1	20
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	22
β-strand	140	1	21
β-strand	144-150	7	23
β-strand	154	1	23
β-strand	159-163	5	22
α-helix	164-167	4
β-strand	173-182	10	22
α-helix	183-186	4
β-strand	191-198	8	23
β-strand	205-210	6	23

Chain C: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	39
β-strand	10-11	2	40
β-strand	18-25	8	39
β-strand	33-39	7	40
β-strand	45-51	7	40
β-strand	57-59	3	40
β-strand	60	1	20
α-helix	61-63	3
β-strand	67-72	6	39
β-strand	77-82	6	39
α-helix	84-86	3
β-strand	88-95	8	40
β-strand	100D-103	4	40
β-strand	107-110	4	40

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	8
α-helix	96	1
β-strand	100	1	9
β-strand	100D-102	3	8
β-strand	107-109	3	8
β-strand	110-111	2	7
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
β-strand	205-211	7	12

Chain F: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
α-helix	27A-28	2
α-helix	29-31	3
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	85-90	6	14
β-strand	97-98	2	14
β-strand	99	1	13
β-strand	102-106	5	14
β-strand	111	1	15
α-helix	112-113	2
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	144-150	7	17
β-strand	153-154	2	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-186	4
β-strand	191-198	8	17
β-strand	205-210	6	17

Chain G: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	41
β-strand	11	1	42
β-strand	18-25	8	41
β-strand	33-39	7	43
β-strand	45-51	7	43
β-strand	57-59	3	43
α-helix	61-63	3
β-strand	67-72	6	41
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-95	8	43
β-strand	100D-103	4	43
β-strand	104	1	41
β-strand	107-109	3	43
β-strand	110	1	42

Chains H and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	9

Chain I: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	24
β-strand	11-12	2	25
β-strand	18-25	8	24
α-helix	29-31	3
β-strand	34-39	6	26
β-strand	45-51	7	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
α-helix	96	1
β-strand	100	1	27
β-strand	100D-102	3	26
β-strand	107-109	3	26
β-strand	110-111	2	25
α-helix	114-116	3
β-strand	117	1	28
α-helix	118-119	2
β-strand	120-124	5	29
α-helix	125-127	3
β-strand	135-145	11	29
β-strand	146	1	28
β-strand	151-154	4	30
α-helix	155-157	3
β-strand	159	1	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	169-170	2	29
β-strand	176-185	10	29
α-helix	186-188	3
β-strand	195-200	6	30
β-strand	205-210	6	30

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3945 Fab heavy chain	A, E, I	protein	224	Homo sapiens
3945 Kappa light chain	B, F, J	protein	215	Homo sapiens
Anti-Kappa VHH domain	C, G, K	protein	121	Lama glama
Circumsporozoite protein	D, H, L	protein	12	Plasmodium falciparum	P19597 (AlphaFold model)

Sequence of entity 1 (A, E, I), FASTA

>6O25_1 3945 Fab heavy chain (chains A, E, I)
QVQLVESGGGVVQPGRSLRLSCEASGFTFSSYGIHWVRQAPGKGLEWVAVIWYDGSNKYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARAGYSNYGHYFDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (B, F, J), FASTA

>6O25_2 3945 Kappa light chain (chains B, F, J)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIP
DRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPPTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, G, K), FASTA

>6O25_3 Anti-Kappa VHH domain (chains C, G, K)
XVQLXXSGGGXVQXGXSLXLSCXAXXXXXXXXXXXWXRQXPGXXREXVXXXXXXXXXXXX
XDSXXGRFTXSXDXXXXXXXLQXXXLXXXDXAXYYCXXXXXXXXXXXXXXWGXGTXVTVS
S

Sequence of entity 4 (D, H, L), FASTA

>6O25_4 Circumsporozoite protein (chains D, H, L)
NANPNANPNANP

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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