5N8J: Streptavidin

CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide GyGlanvdessG. Determined by X-ray diffraction at 1.05 Å resolution. Released 25 Oct 2017.

Method: X-ray diffraction
Resolution: 1.05 Å
Organisms: Streptomyces avidinii, synthetic construct
Chains: 7
Atoms: 4,571
Mol. weight: 78.96 kDa
Ligands: IPA
Released: 25 Oct 2017

Explore 5N8J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N8J contains 14 α-helices and 32 β-strands across 7 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 and D: 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	113	1
α-helix	116-121	6
β-strand	123-131	9	1

Chain B: 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
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	113	1
α-helix	116-121	6
β-strand	123-131	9	1

Chain 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	54-60	7	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

Chains E and O: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, C, D	protein	183	Streptomyces avidinii	P22629 (AlphaFold model)
Gly-dty-gly-dle-dal-dsg-dva-das-dgl-dsn-dsn-gly	E, O, P	protein	12	synthetic construct

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

>5N8J_1 Streptavidin (chains A, B, C, D)
MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGAD
GALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQY
VGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDA
VQQ

Sequence of entity 2 (E, O, P), FASTA

>5N8J_2 GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY (chains E, O, P)
GYGLANVDESSG

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1

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
4CPE 1.06 Å, Wild-type streptavidin in complex with love-hate ligand 1 (LH1)

Browse structure collections

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