3X3F: Heavy chain of KMTR2

TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2. Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,199
Mol. weight: 64.94 kDa
Ligands: NAG
Released: 23 Dec 2015

Explore 3X3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3X3F contains 24 α-helices and 56 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	77	1	12
β-strand	80	1	12
β-strand	81	1	13
β-strand	85-87	3	14
β-strand	94-96	3	14
α-helix	97-98	2
β-strand	102-103	2	15
β-strand	108	1	13
β-strand	110	1	8
α-helix	113	1
β-strand	114-115	2	15
α-helix	116-120	5
β-strand	123-127	5	16
β-strand	130	1	17
β-strand	133	1	17
β-strand	136-139	4	16

Chain H: 12 helices, 21 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
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	46-52	7	2
β-strand	57-59	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
α-helix	103-105	3
β-strand	116	1	2
β-strand	120-124	5	2
α-helix	127-129	3
β-strand	130	1	3
α-helix	131-132	2
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	176-178	3	4
α-helix	179-181	3
β-strand	182-183	2	4
β-strand	189-198	10	4
α-helix	199-202	4
β-strand	208-213	6	5
α-helix	214-216	3
β-strand	218-223	6	5

Chain L: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	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
β-strand	93	1	8
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
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-197	7	11
β-strand	205-210	6	11

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)
Tumor necrosis factor receptor superfamily member 10B	A	protein	142	Homo sapiens	O14763 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>3X3F_1 Heavy chain of KMTR2 (chains H)
QVQLVQSGAEMKKPGASVKVSCKTSGYTFTNYKINWVRQAPGQGLEWMGWMNPDTDSTGY
PQKFQGRVTMTRNTSISTAYMELSSLRSEDTAVYYCARSYGSGSYYRDYYYGMDVWGQGT
TVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYG

Sequence of entity 2 (L), FASTA

>3X3F_2 Light chain of KMTR2 (chains L)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPLTFGGGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>3X3F_3 Tumor necrosis factor receptor superfamily member 10B (chains A)
ALITQQDLAPQQRVAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFC
LRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPW
SDIECVHKESGSRADYKDDDDK

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 (GOL, 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
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
3X3G 2.51 Å, Fab fragment from anti TRAIL-R2 Human Agonist Antibody KMTR2
6WIB 2.55 Å, Next generation monomeric IgG4 Fc

Browse structure collections

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