3DUU: SAG506-01, orthorhombic, twinned, crystal 2

Crystal structure of SAG506-01, orthorhombic, twinned, crystal 2. Determined by X-ray diffraction at 1.95 Å resolution. Released 2 Dec 2008.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Mus Musculus
Chains: 4
Atoms: 3,879
Mol. weight: 52.53 kDa
Ligands: MG, KDO
Released: 2 Dec 2008

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

Secondary structure: helices and β-sheets

3DUU contains 7 α-helices and 53 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.

Chain A: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	18-25	8	1
β-strand	27C-27D	2	3
β-strand	30-31	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: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	10-12	3	5
β-strand	17-25	9	4
α-helix	29-31	3
β-strand	33-39	7	6
β-strand	46-51	6	6
β-strand	57-59	3	6
β-strand	64	1	4
β-strand	67-72	6	4
β-strand	77-82A	7	4
β-strand	89-95	7	6
β-strand	102-103	2	6
β-strand	107-108	2	6
β-strand	109-111	3	5

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	7
β-strand	10-13	4	8
β-strand	19-24	6	7
β-strand	27C-27D	2	9
β-strand	30-31	2	9
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
β-strand	96-97	2	8
β-strand	101-105	5	8

Chain D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	46-51	6	12
β-strand	57-59	3	12
β-strand	64	1	13
β-strand	67	1	13
β-strand	68-72	5	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	103	1	12
β-strand	107-109	3	12
β-strand	110-111	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
antibody Fv fragment SAG506-01	A, C	protein	112	Mus Musculus	A0N262 (AlphaFold model)
Ig-like protein	B, D	protein	121	Mus Musculus	A2NU21 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3DUU_1 antibody Fv fragment SAG506-01 (chains A, C)
DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTINGVQAEDLAVYYCKQSYNLRTFGGGTKLELK

Sequence of entity 2 (B, D), FASTA

>3DUU_2 Ig-like protein (chains B, D)
EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTV
EYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDGYYVDAMDYWGQGTSVTVS
S

Ligands and cofactors

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

Other PDB entries of the same protein (UniProt A0N262 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DUS 1.95 Å, Crystal structure of SAG506-01, orthorhombic, twinned, crystal 1
3DV4 1.95 Å, Crystal structure of SAG506-01, tetragonal, crystal 1
3DV6 1.95 Å, Crystal structure of SAG506-01, tetragonal, crystal 2

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