5N8B: Streptavidin with peptide afpdylaeyhgg

Crystal structure of streptavidin with peptide afpdylaeyhgg. Determined by X-ray diffraction at 1.03 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 1.03 Å
Organisms: Streptomyces avidinii, synthetic construct
Chains: 8
Atoms: 5,153
Mol. weight: 80.75 kDa
Released: 4 Oct 2017

Explore 5N8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N8B contains 17 α-helices and 32 β-strands across 8 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, B and G: 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
α-helix	50-52	3
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	116-121	6
β-strand	123-131	9	1

Chains C, E, F and H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-10	3

Chain D: 3 helices, 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
α-helix	50-52	3
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	116-121	6
β-strand	123-131	9	2
α-helix	135-137	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, D, G	protein	183	Streptomyces avidinii	P22629 (AlphaFold model)
Ala-phe-pro-asp-tyr-leu-ala-glu-tyr-his-gly-gly-NH2	C, E, F, H	protein	13	synthetic construct

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

>5N8B_1 Streptavidin (chains A, B, D, G)
MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGAD
GALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQY
VGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDA
VQQ

Sequence of entity 2 (C, E, F, H), FASTA

>5N8B_2 ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2 (chains C, E, F, H)
AFPDYLAEYHGGX

Primary citation

Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target. Lyamichev, V.I., Goodrich, L.E., Sullivan, E.H. et al. Sci Rep (2017) 7:12116-12116. DOI 10.1038/s41598-017-12440-1 · 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
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)

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