5D3D: Staphylococcal Superantigen-Like protein 3

Crystal structure of Staphylococcal Superantigen-Like protein 3. Determined by X-ray diffraction at 1.94 Å resolution. Released 19 Aug 2015.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Staphylococcus aureus (strain NCTC 8325)
Chains: 2
Atoms: 3,521
Mol. weight: 46.44 kDa
Ligands: SCN
Released: 19 Aug 2015

Explore 5D3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D3D contains 18 α-helices and 30 β-strands across 2 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: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	139-144	6
β-strand	150-157	8	1
β-strand	158	1	2
β-strand	168-171	4	2
β-strand	178-181	4	2
α-helix	185-189	5
β-strand	195-202	8	1
α-helix	204-206	3
β-strand	215-216	2	2
β-strand	219-221	3	1
α-helix	222-223	2
β-strand	229-238	10	3
β-strand	244-253	10	3
β-strand	257-259	3	4
α-helix	260-275	16
β-strand	277	1	5
β-strand	281	1	5
β-strand	284-290	7	3
β-strand	295-299	5	3
α-helix	303-305	3
α-helix	306-310	5
β-strand	312-314	3	4
α-helix	315-317	3
β-strand	318-325	8	3

Chain B: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
α-helix	139-144	6
β-strand	150-157	8	6
β-strand	158	1	7
α-helix	160	1
α-helix	163	1
β-strand	168-171	4	7
β-strand	178-181	4	7
α-helix	184-188	5
β-strand	195-202	8	6
β-strand	215-216	2	7
β-strand	219-221	3	6
α-helix	222-223	2
β-strand	229-238	10	8
β-strand	244-253	10	8
β-strand	257-259	3	9
α-helix	260-275	16
β-strand	284-290	7	8
β-strand	295-299	5	8
α-helix	303-305	3
α-helix	306-310	5
β-strand	312-314	3	9
α-helix	315-317	3
β-strand	318-325	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Staphylococcal Superantigen-Like protein 3	A, B	protein	195	Staphylococcus aureus (strain NCTC 8325)	Q2G0X7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5D3D_1 Staphylococcal Superantigen-Like protein 3 (chains A, B)
GSMTPKYEDLRAYYTKPSFEFEKQFGFMLKPWTTVRFMNVIPNRFIYKIALVGKDEKKYK
DGPYDNIDVFIVLEDNKYQLKKYSVGGITKTNSKKVNHKVELSITKKDNQGMISRDVSEY
MITKEEISLKELDFKLRKQLIEKHNLYGNMGSGTIVIKMKNGGKYTFELHKKLQEHRMAD
VIDGTNIDNIEVNIK

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	2

Water and common crystallization additives (NA, GOL, CL) are not listed.

Primary citation

Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3). Koymans, K.J., Feitsma, L.J., Brondijk, T.H. et al. Proc Natl Acad Sci U S A (2015) 112:11018-11023. DOI 10.1073/pnas.1502026112 · PubMed

Other PDB entries of the same protein (UniProt Q2G0X7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5I4D 1.75 Å, 1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from…
5D3I 3.2 Å, Crystal structure of the SSL3-TLR2 complex

Browse structure collections

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