6GH7: Streptavidin

WILDTYPE CORE-STREPTAVIDIN WITH a conjugated BIOTINYLATED PYRROLIDINE. Determined by X-ray diffraction at 1.08 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 1.08 Å
Organism: Streptomyces avidinii
Chains: 4
Atoms: 4,366
Mol. weight: 54.9 kDa
Ligands: EYW
Released: 10 Oct 2018

Explore 6GH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GH7 contains 8 α-helices and 32 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.

Chains A and C: 2 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
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

Chains B and D: 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	119-121	3
β-strand	123-131	9	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptavidin	A, B, C, D	protein	128	Streptomyces avidinii	P22629 (AlphaFold model)

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

>6GH7_1 Streptavidin (chains A, B, C, D)
MAEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGT
ALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFT
KVKPSAAS

Ligands and cofactors

ID	Name	Formula	Copies
EYW	5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothi…	C14 H24 N4 O2 S	4

Primary citation

Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host. Nodling, A.R., Swiderek, K., Castillo, R. et al. Angew Chem Int Ed Engl (2018) 57:12478-12482. DOI 10.1002/anie.201806850 · 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…

Browse structure collections

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