5N8W: Streptavidin

CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing peptide GGwhdeatwkpG. Determined by X-ray diffraction at 1.1 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 1.1 Å
Organisms: Streptomyces avidinii, synthetic construct
Chains: 4
Atoms: 2,502
Mol. weight: 40.93 kDa
Released: 4 Oct 2017

Explore 5N8W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N8W contains 7 α-helices and 16 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: 3 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
α-helix	134-135	2

Chain B: 2 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

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B	protein	183	Streptomyces avidinii	P22629 (AlphaFold model)
Gly-gly-dtr-dhi-das-dgl-dal-dth-dtr-dly	C, D	protein	14	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5N8W_1 Streptavidin (chains A, B)
MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGAD
GALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQY
VGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDA
VQQ

Sequence of entity 2 (C, D), FASTA

>5N8W_2 GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY (chains C, D)
GGWHDEATWKPGLY

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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