4LKX: Humanized antibody 4B12 Fab

Humanized antibody 4B12 Fab complexed with a CemX segment. Determined by X-ray diffraction at 1.92 Å resolution. Released 29 Jan 2014.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,629
Mol. weight: 49.09 kDa
Released: 29 Jan 2014

Explore 4LKX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LKX contains 19 α-helices and 45 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 A: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
β-strand	34-39	7	2
β-strand	46-52	7	2
β-strand	57-59	3	2
α-helix	64-66	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	88-96	9	2
β-strand	99-103	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
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	186-189	4
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5
α-helix	212-214	3

Chain B: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	27C	1	8
β-strand	31	1	8
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	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
α-helix	155	1
β-strand	159-163	5	10
β-strand	173-182	10	10
α-helix	183-188	6
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain R: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	13-14	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment heavy chain	A	protein	225	Homo sapiens	Q6GMX6 (AlphaFold model)
Fab fragment light chain	B	protein	219	Homo sapiens	Q0KKI6 (AlphaFold model)
CemX segment	R	protein	14	Homo sapiens

Sequence of entity 1 (A), FASTA

>4LKX_1 Fab fragment heavy chain (chains A)
QVQLQESGPGLVKPSETLSLTCTVSGYSITSDYAWNWIRQPPGKGLEWIGSISYSGITGY
NPSLKSRVTISRDTSKNQFSLKLSSVTAADTAVYYCARMGYDGLAYWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKTHT

Sequence of entity 2 (B), FASTA

>4LKX_2 Fab fragment light chain (chains B)
DIVMTQTPLSLSVTPGQPASISCRSSQSIVHSNGNTYLEWYLQKPGQSPQLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPPTFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>4LKX_3 CemX segment (chains R)
LAGGSAQSQRAPDR

Primary citation

Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations. Chu, H.M., Wright, J., Chan, Y.H. et al. Nat Commun (2014) 5:3139-3139. DOI 10.1038/ncomms4139 · 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
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
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
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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