5VR9: CH1/Ckappa Fab based on Matuzumab

CH1/Ckappa Fab based on Matuzumab. Determined by X-ray diffraction at 2.15 Å resolution. Released 2 Aug 2017.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,868
Mol. weight: 94.85 kDa
Released: 2 Aug 2017

Explore 5VR9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VR9 contains 36 α-helices and 87 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: 10 helices, 22 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
β-strand	34-39	6	2
β-strand	46-51	6	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	107-111	5	2
β-strand	115-119	5	2
α-helix	123-124	2
β-strand	125	1	3
α-helix	126-127	2
β-strand	128-132	5	4
β-strand	143-153	11	4
β-strand	154	1	3
β-strand	159-162	4	5
α-helix	163-165	3
β-strand	167	1	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	177-178	2	4
α-helix	179	1
β-strand	184-193	10	4
α-helix	194-196	3
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
β-strand	10-13	4	7
β-strand	19-24	6	6
β-strand	33-37	5	7
α-helix	42-43	2
β-strand	44-48	5	7
β-strand	52-53	2	7
α-helix	54	1
β-strand	61-66	6	6
β-strand	69-74	6	6
α-helix	79-81	3
β-strand	83-91	9	7
β-strand	94-97	4	7
β-strand	101-105	5	7
β-strand	110	1	8
α-helix	111-112	2
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	9
β-strand	139	1	8
β-strand	144-149	6	10
β-strand	152-153	2	10
α-helix	154	1
β-strand	158-162	5	9
α-helix	163-166	4
β-strand	172-181	10	9
α-helix	182-186	5
β-strand	190-196	7	10
β-strand	204-209	6	10

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	10-12	3	12
β-strand	18-25	8	11
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-101	10	12
β-strand	107-111	5	12
β-strand	115-119	5	12
α-helix	123-124	2
β-strand	125	1	13
α-helix	126-127	2
β-strand	128-132	5	14
β-strand	139	1	14
β-strand	143-153	11	14
β-strand	154	1	13
β-strand	159-162	4	15
α-helix	163-165	3
β-strand	167	1	15
β-strand	171-173	3	14
α-helix	174-176	3
β-strand	177-178	2	14
β-strand	184-193	10	14
α-helix	194-196	3
β-strand	203-208	6	15
α-helix	209-211	3
β-strand	213-218	6	15

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	7
β-strand	19-25	7	16
β-strand	31-37	7	7
β-strand	44-48	5	7
β-strand	52-53	2	7
α-helix	54	1
β-strand	61-66	6	16
β-strand	69-74	6	16
α-helix	79-81	3
β-strand	83-91	9	7
β-strand	94-97	4	7
β-strand	101-106	6	7
β-strand	110	1	17
α-helix	111-112	2
β-strand	113-117	5	18
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	18
β-strand	139	1	17
β-strand	144-149	6	19
β-strand	152-153	2	19
α-helix	154	1
β-strand	158-162	5	18
α-helix	163-166	4
β-strand	172-181	10	18
α-helix	182-186	5
β-strand	190-196	7	19
β-strand	204-209	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CH1/Ckappa Fab heavy chain	A, H	protein	224	Homo sapiens	Q6GMX6 (AlphaFold model)
CH1/Ckappa Fab light chain	B, L	protein	212	Homo sapiens	Q7Z3Y4 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5VR9_1 CH1/Ckappa Fab heavy chain (chains A, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSHWMHWVRQAPGQGLEWIGEFNPSNGRTNY
NEKFKSKATMTVDTSTNTAYMELSSLRSEDTAVYYCASRDYDYDGRYFDYWGQGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (B, L), FASTA

>5VR9_2 CH1/Ckappa Fab light chain (chains B, L)
DIQMTQSPSSLSASVGDRVTITCSASSSVTYMYWYQQKPGKAPKLLIYDTSNLASGVPSR
FSGSGSGTDYTFTISSLQPEDIATYYCQQWSSHIFTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Primary citation

Computational design of a specific heavy chain/ kappa light chain interface for expressing fully IgG bispecific antibodies. Froning, K.J., Leaver-Fay, A., Wu, X. et al. Protein Sci (2017) 26:2021-2038. DOI 10.1002/pro.3240 · PubMed

Other PDB entries of the same protein (UniProt Q6GMX6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
4NPY 1.8 Å, Crystal structure of germline Fab PGT121, a putative precursor of the broadly reactive…
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4LKX 1.92 Å, Humanized antibody 4B12 Fab complexed with a CemX segment
3ZL4 1.95 Å, Antibody structural organization: Role of kappa - lambda chain constant domain switch in…
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
6VPY 2.36 Å, I33M (I3.2 mutant from CH103 Lineage)
4FQQ 2.42 Å, Crystal Structure of Germline Antibody PGT121-GL Fab
6AL4 2.45 Å, Crystal structure of anti-CD19 antibody B43 FAB
4D9L 2.48 Å, Fab structure of anti-HIV-1 gp120 V2 mAb 697
5UTZ 2.75 Å, Human IL-2/Fab complex

Browse structure collections

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