3DUR: SAG173-04

Crystal structure of SAG173-04. Determined by X-ray diffraction at 1.86 Å resolution. Released 2 Dec 2008.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Mus musculus
Chains: 4
Atoms: 4,132
Mol. weight: 52.4 kDa
Ligands: KDO, MG
Released: 2 Dec 2008

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

Secondary structure: helices and β-sheets

3DUR contains 10 α-helices and 50 β-strands across 4 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.

Chains A and C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	18-25	8	1
β-strand	30-30A	2	3
β-strand	30F-31	2	3
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	70-76	7	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	96-97	2	2
β-strand	101-105	5	2

Chain B: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11-12	2	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	33-39	7	6
β-strand	46-51	6	6
α-helix	52B-52D	3
β-strand	55-57	3	6
β-strand	62	1	4
β-strand	65-70	6	4
β-strand	75-80	6	4
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	100E-101	2	6
β-strand	105-107	3	6
β-strand	108-109	2	5

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	46-51	6	11
α-helix	52B-52D	3
β-strand	55-57	3	11
β-strand	65-70	6	10
β-strand	75-80A	6	10
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	100E-101	2	11
β-strand	105-109	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody Fv fragment SAG173-04	A, C	protein	112	Mus musculus	A2N494 (AlphaFold model)
Ig-like protein	B, D	protein	121	Mus musculus	A2NU21 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3DUR_1 antibody Fv fragment SAG173-04 (chains A, C)
DIVMTQSPSSLAVSAGEKVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYNLRTFGGGTKLELK

Sequence of entity 2 (B, D), FASTA

>3DUR_2 Ig-like protein (chains B, D)
EVQLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTT
EYSASVKGRFSISRDNSQSILYLQMNTLRAEDSATYYCARDGYYADAMDYWGQGTSVTVS
S

Ligands and cofactors

ID	Name	Formula	Copies
KDO	3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid	C8 H14 O8	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (PG4) are not listed.

Primary citation

Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments. Brooks, C.L., Blackler, R.J., Gerstenbruch, S. et al. Acta Crystallogr D Biol Crystallogr (2008) 64:1250-1258. DOI 10.1107/S0907444908033453 · PubMed

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