5N7X: Streptavidin with peptide ewvhpqfeqkak

Crystal structure of streptavidin with peptide ewvhpqfeqkak. Determined by X-ray diffraction at 1.12 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 1.12 Å
Organisms: Streptomyces avidinii, Homo sapiens
Chains: 16
Atoms: 9,634
Mol. weight: 163.04 kDa
Released: 4 Oct 2017

Explore 5N7X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N7X contains 17 α-helices and 64 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, E, H, K and M: 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	53-60	8	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

Chain F: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	4
β-strand	28-33	6	4
β-strand	38-44	7	4
α-helix	50-52	3
β-strand	53-60	8	4
β-strand	71-80	10	4
β-strand	85-97	13	4
β-strand	103-112	10	4
α-helix	119-121	3
β-strand	123-131	9	4

Chain O: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	3
β-strand	28-33	6	3
β-strand	38-44	7	3
α-helix	50-52	3
β-strand	53-60	8	3
β-strand	71-80	10	3
β-strand	85-97	13	3
β-strand	103-112	10	3
α-helix	113	1
α-helix	119-121	3
β-strand	123-131	9	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, E, F, H, K, M, O	protein	183	Streptomyces avidinii	P22629 (AlphaFold model)
Glu-trp-val-his-pro-gln-phe-glu-gln-lys-ala-lys peptide	C, D, G, I, J, L, N, P	protein	12	Homo sapiens

Sequence of entity 1 (A, B, E, F, H, K, M, O), FASTA

>5N7X_1 Streptavidin (chains A, B, E, F, H, K, M, O)
MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGAD
GALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQY
VGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDA
VQQ

Sequence of entity 2 (C, D, G, I, J, L, N, P), FASTA

>5N7X_2 GLU-TRP-VAL-HIS-PRO-GLN-PHE-GLU-GLN-LYS-ALA-LYS Peptide (chains C, D, G, I, J, L, N, P)
EWVHPQFEQKAK

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
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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