1HA5: Streptococcal pyogenic exotoxin A1

Name: PDB 1HA5: Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition.
Published: 2002-04-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Determined by X-ray diffraction at 2.82 Å resolution. Released 3 Apr 2002.

Method: X-ray diffraction
Resolution: 2.82 Å
Organism: STREPTOCOCCUS PYOGENES
Chains: 4
Atoms: 7,180
Mol. weight: 101.77 kDa
Ligands: ZN
Released: 3 Apr 2002

Explore 1HA5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1HA5 contains 30 α-helices and 74 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	1010-1011	2
α-helix	1012-1014	3
α-helix	1019-1026	8
β-strand	1030-1036	7	1
β-strand	1039	1	2
β-strand	1045-1048	4	2
β-strand	1052	1	3
β-strand	1055	1	3
β-strand	1057-1061	5	2
α-helix	1065-1069	5
β-strand	1075-1080	6	1
β-strand	1083	1	2
β-strand	1096-1100	5	2
β-strand	1103-1105	3	1
β-strand	1110-1123	14	4
β-strand	1126-1137	12	4
β-strand	1139-1141	3	5
α-helix	1142-1157	16
β-strand	1161	1	6
β-strand	1163	1	6
β-strand	1169-1175	7	4
α-helix	1180-1181	2
β-strand	1182-1185	4	4
α-helix	1194-1198	5
α-helix	1199-1201	3
β-strand	1206-1208	3	5
β-strand	1213-1219	7	4

Chain B: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2006-2008	3
α-helix	2012-2014	3
α-helix	2020-2026	7
α-helix	2028-2029	2
β-strand	2030-2035	6	7
β-strand	2039	1	8
β-strand	2045-2048	4	8
β-strand	2052	1	9
β-strand	2055	1	9
β-strand	2057-2061	5	8
α-helix	2065-2070	6
β-strand	2076-2080	5	7
β-strand	2083	1	8
β-strand	2096-2100	5	8
β-strand	2103-2105	3	7
β-strand	2115-2123	9	10
β-strand	2126-2135	10	10
β-strand	2139-2141	3	11
α-helix	2142-2157	16
β-strand	2169-2175	7	10
β-strand	2182-2185	4	10
α-helix	2194-2197	4
α-helix	2198-2201	4
β-strand	2206-2208	3	11
β-strand	2213-2219	7	10

Chain C: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3010-3011	2
α-helix	3012-3014	3
α-helix	3019-3026	8
β-strand	3030-3036	7	12
β-strand	3039	1	13
β-strand	3045-3048	4	13
β-strand	3052	1	14
β-strand	3055	1	14
β-strand	3057-3061	5	13
α-helix	3065-3072	8
β-strand	3075-3080	6	12
β-strand	3083	1	13
β-strand	3096-3100	5	13
β-strand	3103-3105	3	12
β-strand	3110-3123	14	15
β-strand	3126-3137	12	15
β-strand	3139-3141	3	16
α-helix	3142-3157	16
β-strand	3169-3174	6	15
α-helix	3180-3181	2
β-strand	3182-3185	4	15
α-helix	3194-3197	4
α-helix	3198-3201	4
β-strand	3206-3208	3	16
β-strand	3214-3219	6	15

Chain D: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	4012-4014	3
α-helix	4019-4026	8
β-strand	4030-4036	7	17
β-strand	4039	1	18
β-strand	4045-4048	4	18
β-strand	4052	1	19
β-strand	4055	1	19
β-strand	4057-4061	5	18
α-helix	4065-4069	5
β-strand	4075-4080	6	17
β-strand	4083	1	18
β-strand	4096-4100	5	18
β-strand	4103-4105	3	17
β-strand	4110-4120	11	20
β-strand	4123	1	20
β-strand	4126	1	20
β-strand	4130-4137	8	20
β-strand	4139-4141	3	21
α-helix	4142-4156	15
β-strand	4161	1	22
β-strand	4163	1	22
β-strand	4170-4175	6	20
β-strand	4182-4185	4	20
α-helix	4194-4197	4
α-helix	4198-4201	4
β-strand	4206-4208	3	21
β-strand	4213-4218	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Streptococcal pyogenic exotoxin A1	A, B, C, D	protein	218	STREPTOCOCCUS PYOGENES	P0DJY7 (AlphaFold model)

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

>1HA5_1 STREPTOCOCCAL PYOGENIC EXOTOXIN A1 (chains A, B, C, D)
DPDPSQLHRSSLVKNLQNIYFLYEGDPVTHENVKSVDQLLSHDLIYNVSGPNYDKLKTEL
KNQEMATLFKDKNVDIYGVEYYHLCYLCENAERSACIYGGVTNHAGNHLEIPKKIVVKVS
IDGIQSLSFDIETNKKMVTAQELDYKVRKYLTDNKQLYTNGPSKYETGYIKFIPKNKESF
WFDFFPEPEFTQSKYLMIYKDNETLDSNTSQIEVYLTT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural Features of a Zinc Binding Site in the Superantigen Strepococcal Pyrogenic Exotoxin a (Spea1): Implications for Mhc Class II Recognition. Baker, M.D., Gutman, D.M., Papageorgiou, A.C. et al. Protein Sci (2001) 10:1268. DOI 10.1110/PS.330101 · PubMed

Other PDB entries of the same protein (UniProt P0DJY7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1L0Y 2.5 Å, T cell receptor beta chain complexed with superantigen SpeA soaked with zinc
1B1Z 2.57 Å, Streptococcal pyrogenic exotoxin A1
1UUP 2.6 Å, Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1).
1L0X 2.8 Å, TCR beta chain complexed with streptococcal superantigen SpeA
1FNV 3.6 Å, Structure of streptococcal pyrogenic exotoxin a
1FNW 3.9 Å, Crystal structure of streptococcal pyrogenic exotoxin a

Browse structure collections

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