8XS1: Fab fragment of anti-osteocalcin antibody KTM219

Crystal structure of Fab fragment of anti-osteocalcin antibody KTM219 complexed with C-terminal peptide antigen. Determined by X-ray diffraction at 2.3 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 3,447
Mol. weight: 52.36 kDa
Released: 15 Jan 2025

Explore 8XS1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XS1 contains 21 α-helices and 45 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: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-23	6	1
α-helix	26-31	6
β-strand	33-40	8	2
β-strand	44-52	9	2
β-strand	56-59	4	2
α-helix	61-63	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	88-95	8	2
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
α-helix	128-130	3
β-strand	131	1	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	157-160	4
β-strand	164-165	2	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	188-191	4
β-strand	195-200	6	5
α-helix	201-203	3
β-strand	205-210	6	5

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
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
α-helix	55	1
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
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 fragment (Fd) chain of anti-osteocalcin antibody KTM219	H	protein	249	Mus musculus
Light chain of anti-osteocalcin antibody KTM219	L	protein	232	Mus musculus
Osteocalcin	A	protein	7	Homo sapiens	P02818 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8XS1_1 Heavy chain fragment (Fd) chain of anti-osteocalcin antibody KTM219 (chains H)
MATGQVKLQQSGAEFVKAGASVKLSCKTSGYTFNNYWIHWVKQSPGQGLEWIGEIDPSDG
YSNYNQKFKGKATLTVDKSSSTAYMHLNSLTSEDSAVYYCTSSTSVGGSWGQGTTVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSASAAHHHHHHGAAEQKLI
SEEDLNGAA

Sequence of entity 2 (L), FASTA

>8XS1_2 Light chain of anti-osteocalcin antibody KTM219 (chains L)
MSDIELTQSPLSLPVSLGDQASISCTSSQSLLHSNGDTYLHWYLQKPGQSPKLLIYTLSN
RFSGVPDRFSGSGSGTDFTLKISRVEAADLGIYFCSQTTHVPYTFGGGTKLEIKRADAAP
SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY
SLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEGGGSDYKDDDDK

Sequence of entity 3 (A), FASTA

>8XS1_3 Osteocalcin (chains A)
RRFYGPV

Primary citation

Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219. Yazaki, S., Komatsu, M., Dong, J. et al. Int J Mol Sci (2025) 26. DOI 10.3390/ijms26020648 · PubMed

Other PDB entries of the same protein (UniProt P02818 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9L23 2.62 Å, cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Osteocalcin
13IB 2.68 Å, Structure of GGCX-BGP-Anisindione complex
9WF2 2.94 Å, Cryo-EM structure of GGCX-BGP complex
9BUR 2.95 Å, Structure of GGCX-BGP complex
9BUX 3.06 Å, Structure of GGCX-BGP-menaquinone-4 epoxide complex
9MQC 3.13 Å, Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K hydroquinone
9MQB 3.37 Å, Vitamin K-dependent gamma-carboxylase with Osteocalcin (mutant) and vitamin K…
9MQE 3.56 Å, Vitamin K-dependent gamma-carboxylase with Osteocalcin and vitamin K hydroquinone

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