1SM3: SM3 antibody

Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope. Determined by X-ray diffraction at 1.95 Å resolution. Released 23 Mar 1999.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,564
Mol. weight: 48.84 kDa
Ligands: CD
Released: 23 Mar 1999

Explore 1SM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SM3 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 H: 10 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	34-40	7	8
β-strand	44-51	8	8
α-helix	52B-53	3
β-strand	57-59	3	8
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	102-103	2	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	175-184	10	10
α-helix	185-187	3
β-strand	193-199	7	11
α-helix	200-202	3
β-strand	204-210	7	11

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-13	4	2
β-strand	19-25	7	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	43-49	7	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	84-91	8	2
β-strand	96-98	3	2
β-strand	99	1	1
β-strand	102-106	5	2
β-strand	111	1	3
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-161	3	4
α-helix	162-164	3
β-strand	165-166	2	4
β-strand	172-181	10	4
α-helix	182-187	6
β-strand	190-197	8	5
β-strand	200-207	8	5

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SM3 antibody	L	protein	215	Mus musculus	P01723 (AlphaFold model)
SM3 antibody	H	protein	218	Mus musculus	P01801 (AlphaFold model)
Peptide epitope	P	protein	13		P15941 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1SM3_1 SM3 ANTIBODY (chains L)
DIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGSEKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCS

Sequence of entity 2 (H), FASTA

>1SM3_2 SM3 ANTIBODY (chains H)
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYAT
HYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSAKT
TPPTVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLASGVHTFPAVLQSDLYT
LSSSVTVPSSTWPSETVTCNVAHPASSTKVDAKIVPRD

Sequence of entity 3 (P), FASTA

>1SM3_3 PEPTIDE EPITOPE (chains P)
TSAPDTRPAPGST

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	8

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

Primary citation

Crystal structure at 1.95 A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition. Dokurno, P., Bates, P.A., Band, H.A. et al. J Mol Biol (1998) 284:713-728. DOI 10.1006/jmbi.1998.2209 · PubMed

Other PDB entries of the same protein (UniProt P01723 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Q0X 1.6 Å, Anti-morphine Antibody 9B1 Unliganded Form
1P4B 2.35 Å, Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide…
3CFJ 2.6 Å, Crystal structure of catalytic elimination antibody 34E4, orthorhombic crystal form
3CFK 2.6 Å, Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form
1P4I 2.8 Å, Crystal Structure of scFv against peptide GCN4

Browse structure collections

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