4GDA: Circular Permuted Streptavidin A50/N49

Circular Permuted Streptavidin A50/N49. Determined by X-ray diffraction at 1.0 Å resolution. Released 5 Jun 2013.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Streptomyces avidinii
Chains: 2
Atoms: 2,455
Mol. weight: 28.18 kDa
Ligands: EOH, BTN
Released: 5 Jun 2013

Explore 4GDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GDA contains 5 α-helices and 16 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 A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	54-60	7	1
β-strand	71-80	10	1
β-strand	85-97	13	1
β-strand	103-112	10	1
α-helix	113	1
α-helix	116-121	6
β-strand	123-132	10	1
α-helix	213-217	5
β-strand	219-223	5	1
β-strand	228-233	6	1
β-strand	238-244	7	1

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	53-60	8	2
β-strand	71-80	10	2
β-strand	85-97	13	2
β-strand	103-112	10	2
α-helix	113	1
α-helix	116-121	6
β-strand	123-131	9	2
β-strand	219-223	5	2
β-strand	228-233	6	2
β-strand	238-244	7	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B	protein	131	Streptomyces avidinii	P22629 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4GDA_1 Streptavidin (chains A, B)
AESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWL
LTSGTTEANAWKSTLVGHDTFTKVKPSAASGGGSAEAGITGTWYNQLGSTFIVTAGADGA
LTGTYESAVGN

Ligands and cofactors

ID	Name	Formula	Copies
EOH	Ethanol	C2 H6 O	1
BTN	Biotin	C10 H16 N2 O3 S	2

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin. Le Trong, I., Chu, V., Xing, Y. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:968-977. DOI 10.1107/S0907444913003855 · PubMed

Other PDB entries of the same protein (UniProt P22629 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2F01 0.85 Å, Epi-biotin complex with core streptavidin
9PUA 0.94 Å, L-Biotin-streptavidin binding
3RY2 0.95 Å, Wild-type core streptavidin-biotin complex at atomic resolution
9PUB 0.95 Å, Biotin-streptavidin binding
1LUQ 0.96 Å, Full Matrix Error Analysis of Streptavidin
2GH7 1.0 Å, Epi-biotin complex with core streptavidin
3WYQ 1.0 Å, Crystal structure of the low-immunogenic core streptavidin mutant LISA-314…
6T2L 1.0 Å, Streptavidin variants harbouring an artificial organocatalyst based cofactor
3RY1 1.03 Å, Wild-type core streptavidin at atomic resolution
5N8B 1.03 Å, Crystal structure of streptavidin with peptide afpdylaeyhgg
5N8J 1.05 Å, CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide…
4CPE 1.06 Å, Wild-type streptavidin in complex with love-hate ligand 1 (LH1)

Browse structure collections

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