9PUB: Biotin-streptavidin binding

Biotin-streptavidin binding. Determined by X-ray diffraction at 0.95 Å resolution. Released 3 Sept 2025.

Method: X-ray diffraction
Resolution: 0.95 Å
Organism: Streptomyces avidinii
Chains: 2
Atoms: 2,418
Mol. weight: 27.14 kDa
Ligands: BTN
Released: 3 Sept 2025

Explore 9PUB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PUB contains 4 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 J: 3 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
α-helix	70	1
β-strand	71-80	10	1
β-strand	85-97	13	1
β-strand	103-112	10	1
α-helix	116-121	6
β-strand	123-132	10	1
α-helix	133-134	2

Chain K: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	2
β-strand	28-33	6	2
β-strand	38-44	7	2
β-strand	54-60	7	2
β-strand	71-80	10	2
β-strand	85-97	13	2
β-strand	103-112	10	2
α-helix	119-121	3
β-strand	123-131	9	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	J, K	protein	127	Streptomyces avidinii	P22629 (AlphaFold model)

Sequence of entity 1 (J, K), FASTA

>9PUB_1 Streptavidin (chains J, K)
AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTA
LGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTK
VKPSAAS

Ligands and cofactors

ID	Name	Formula	Copies
BTN	Biotin	C10 H16 N2 O3 S	2

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

Primary citation

Protein chirality as a determinant of ligand affinity: insights from l- and d-streptavidin. Giesler, R.J., Woodham, P.C.S., Draper, S.R.E. et al. Chem Sci (2025) 16:23342-23350. DOI 10.1039/d5sc06380a · 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
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…
4CPE 1.06 Å, Wild-type streptavidin in complex with love-hate ligand 1 (LH1)

Browse structure collections

About this viewer

MolViewer shows 9PUB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.