5I4D: Superantigen-like protein

1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX. Determined by X-ray diffraction at 1.75 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Staphylococcus aureus
Chains: 2
Atoms: 4,379
Mol. weight: 80.79 kDa
Ligands: NAG
Released: 24 Feb 2016

Explore 5I4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I4D contains 15 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	169-174	6
β-strand	180-187	8	1
β-strand	188	1	2
β-strand	198-201	4	2
β-strand	208-211	4	2
α-helix	216-219	4
β-strand	225-232	8	1
β-strand	244-246	3	2
β-strand	249-251	3	1
α-helix	252-253	2
β-strand	259-268	10	3
β-strand	274-283	10	3
β-strand	287-289	3	4
α-helix	290-305	16
β-strand	314-320	7	3
β-strand	325-329	5	3
α-helix	333-335	3
α-helix	336-340	5
β-strand	342-344	3	4
α-helix	345-347	3
β-strand	348-355	8	3

Chain B: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	165-166	2
α-helix	169-175	7
β-strand	180-187	8	5
β-strand	188-189	2	6
β-strand	198-201	4	6
β-strand	208-211	4	6
α-helix	216-219	4
β-strand	225-232	8	5
β-strand	244-246	3	6
β-strand	249-251	3	5
α-helix	252-253	2
β-strand	259-268	10	7
β-strand	274-283	10	7
β-strand	287-289	3	8
α-helix	290-305	16
β-strand	307	1	9
β-strand	311	1	9
β-strand	314-320	7	7
β-strand	325-329	5	7
α-helix	333-335	3
α-helix	336-339	4
β-strand	342-344	3	8
α-helix	345-347	3
β-strand	348-355	8	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Superantigen-like protein	A, B	protein	343	Staphylococcus aureus	Q2G0X7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5I4D_1 Superantigen-like protein (chains A, B)
MGSSHHHHHHENLYFQGEKIQSTKVDKVPTLKAERLAMINITAGANSATTQAANTRQERT
PKLEKAPNTNEEKTSASKIEKISQPKQEEQKTLNISATPAPKQEQSQTTTESTTPKTKVT
TPPSTNTPQPMQSTKSDTPQSPTIKQAQTDMTPKYEDLRAYYTKPSFEFEKQFGFMLKPW
TTVRFMNVIPNRFIYKIALVGKDEKKYKDGPYDNIDVFIVLEDNKYQLKKYSVGGITKTN
SKKVNHKVELSITKKDNQGMISRDVSEYMITKEEISLKELDFKLRKQLIEKHNLYGNMGS
GTIVIKMKNGGKYTFELHKKLQEHRMADVIDGTNIDNIEVNIK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (PG4, PGE) are not listed.

Primary citation

1.75 Angstrom Crystal Structure of Superantigen-like Protein, Exotoxin from Staphylococcus aureus, in Complex with Sialyl-LewisX. Minasov, G., Nocadello, S., Shuvalova, L. et al. To be published.

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

5D3D 1.94 Å, Crystal structure of Staphylococcal Superantigen-Like protein 3
5D3I 3.2 Å, Crystal structure of the SSL3-TLR2 complex

Browse structure collections

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