3X3G: Heavy chain of KMTR2

Fab fragment from anti TRAIL-R2 Human Agonist Antibody KMTR2. Determined by X-ray diffraction at 2.51 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.51 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,424
Mol. weight: 48.77 kDa
Ligands: NAG
Released: 23 Dec 2015

Explore 3X3G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3X3G contains 17 α-helices and 43 β-strands across 2 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: 8 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
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	45-52	8	2
β-strand	57-59	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	92-100	9	2
α-helix	107-110	4
β-strand	115-116	2	2
β-strand	120-124	5	2
β-strand	130	1	3
β-strand	133-137	5	4
β-strand	148-158	11	4
β-strand	159	1	3
β-strand	164-167	4	5
α-helix	168-170	3
β-strand	172	1	5
β-strand	176-178	3	4
α-helix	179-181	3
β-strand	182-183	2	4
α-helix	184	1
β-strand	189-198	10	4
α-helix	199-201	3
β-strand	207-213	7	5
β-strand	218-224	7	5

Chain L: 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
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
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	98	1	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	153-155	3	10
β-strand	159-163	5	9
α-helix	164-165	2
α-helix	167	1
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of KMTR2	H	protein	229	Homo sapiens	P01861 (AlphaFold model)
Light chain of KMTR2	L	protein	214	Homo sapiens	V9HW34 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>3X3G_1 Heavy chain of KMTR2 (chains H)
QVQLVQSGAEMKKPGASVKVSCKTSGYTFTNYKINWVRQAPGQGLEWMGWMNPDTDSTGY
PQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCARSYGSGSYYRDYYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYG

Sequence of entity 2 (L), FASTA

>3X3G_2 Light chain of KMTR2 (chains L)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

TRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2. Tamada, T., Shinmi, D., Ikeda, M. et al. Sci Rep (2015) 5:17936-17936. DOI 10.1038/srep17936 · PubMed

Other PDB entries of the same protein (UniProt P01861 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EO0 1.75 Å, Structure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
4B53 1.8 Å, Crystal structure of the isolated IgG4 CH3 domain
5W5N 1.85 Å, Crystal structure of human IgG4-Sigma2 Fc fragment
4C54 1.9 Å, Crystal structure of recombinant human IgG4 Fc
5W5M 1.9 Å, Crystal structure of human IgG4-Sigma1 Fc fragment
5HVW 1.95 Å, Monomeric IgG4 Fc
3X3F 2.1 Å, TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody…
6WMH 2.3 Å, Next generation monomeric IgG4 Fc
4C55 2.35 Å, Crystal structure of serum-derived human IgG4 Fc
6WNA 2.4 Å, Next generation monomeric IgG4 Fc
6WOL 2.49 Å, Next generation monomeric IgG4 Fc bound to neonatal Fc receptor
6WIB 2.55 Å, Next generation monomeric IgG4 Fc

Browse structure collections

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