3DSF: Anti-osteopontin antibody 23C3

Crystal structure of anti-osteopontin antibody 23C3 in complex with W43A mutated epitope peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 14 Oct 2008.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,352
Mol. weight: 48.19 kDa
Released: 14 Oct 2008

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

Secondary structure: helices and β-sheets

3DSF contains 10 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: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
α-helix	54-56	3
β-strand	60-62	3	8
β-strand	70-75	6	6
β-strand	80-85	6	6
α-helix	90-92	3
β-strand	94-100	7	8
β-strand	106	1	8
β-strand	110-112	3	8
β-strand	113-114	2	7
α-helix	117-119	3
β-strand	120	1	9
α-helix	121-122	2
β-strand	123-127	5	10
β-strand	138-148	11	10
β-strand	149	1	9
β-strand	154-157	4	11
α-helix	158-160	3
β-strand	166-168	3	10
β-strand	173	1	10
β-strand	178-187	10	10
β-strand	197-202	6	11
β-strand	207-212	6	11

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	98	1	2
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	122-125	4
β-strand	130-139	10	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-155	3	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-181	9	4
β-strand	191-197	7	5
β-strand	205-210	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab fragment of anti-osteopontin antibody 23C3, Light chain	L	protein	213	Mus musculus
Fab fragment of anti-osteopontin antibody 23C3, Heavy chain	H	protein	216	Mus musculus
a peptide from osteopontin	P	protein	12		P10451 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3DSF_1 Fab fragment of anti-osteopontin antibody 23C3, Light chain (chains L)
YIQMTQSPASLSVSVGETVTITCRASENIYSFLAWYQQKQGKSPQLLVYAATNLADGVPS
RFSGSGSGTQFSLKINSLQSEDFGTYYCQHFWGTPFTFGSGTKLEIKRSDAAPTVSIFPP
SAAQLSSGGGSVVCFLNNFYPKDINVKWKIDGAERGNGVLNSWTSQDSADSTYSMSSTLT
SGGDEYERHNSYTCEATHKTSTSPIVKSFNRAA

Sequence of entity 2 (H), FASTA

>3DSF_2 Fab fragment of anti-osteopontin antibody 23C3, Heavy chain (chains H)
EVQLVESGGGLVQPKGSLKISCAASGFTFNIYAMNWVRQAPGKGLEWVARIRSQSNNYTT
YYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRQMGDYWGQGTTLTVSSAVKT
PPSVYPLAPGGGAISNSMVTLGCLVNGYFPEPVTVTWNAGSLGSGVHTFPAVLQSDLYTL
SSSVTVPVSTWPSEAVTCNVAHPASATSVDKAISPV

Sequence of entity 3 (P), FASTA

>3DSF_3 a peptide from osteopontin (chains P)
VATALNPDPSQK

Primary citation

Molecular basis of recognition of human osteopontin by 23C3, a potential therapeutic antibody for treatment of rheumatoid arthritis. Du, J., Hou, S., Zhong, C. et al. J Mol Biol (2008) 382:835-842. DOI 10.1016/j.jmb.2008.07.075 · PubMed

Other PDB entries of the same protein (UniProt P10451 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EOU 1.55 Å, Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.
3CXD 2.8 Å, Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide

Browse structure collections

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