1RXJ: Streptavidin

Crystal structure of streptavidin mutant (M2) where the L3,4 loop was replace by that of avidin. Determined by X-ray diffraction at 1.14 Å resolution. Released 11 May 2004.

Method: X-ray diffraction
Resolution: 1.14 Å
Organism: Streptomyces avidinii
Chains: 4
Atoms: 4,257
Mol. weight: 52.98 kDa
Ligands: BNI
Released: 11 May 2004

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

Secondary structure: helices and β-sheets

1RXJ contains 8 α-helices and 32 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	1
β-strand	28-33	6	1
β-strand	38-44	7	1
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	123-131	9	1

Chains B and C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	2
β-strand	28-33	6	2
β-strand	38-44	7	2
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

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	1
β-strand	28-33	6	1
β-strand	38-44	7	1
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	123-131	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, C, D	protein	121	Streptomyces avidinii	P22629 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1RXJ_1 Streptavidin (chains A, B, C, D)
AGITGTWYNQLGSTFIVTAGADGALTGTYESATSNEIKRYVLTGRYDSAPATDGSGTALG
WTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK
P

Ligands and cofactors

ID	Name	Formula	Copies
BNI	5-(2-oxo-hexahydro-THIENO[3,4-d]imidazol-6-yl)-pentanoic acid…	C16 H20 N4 O4 S	4

Primary citation

Structural elements responsible for conversion of streptavidin to a pseudoenzyme. Eisenberg-Domovich, Y., Pazy, Y., Nir, O. et al. Proc Natl Acad Sci U S A (2004) 101:5916-5921. DOI 10.1073/pnas.0308541101 · 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…
4GDA 1.0 Å, Circular Permuted Streptavidin A50/N49
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…

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