7PC8: The PDZ domain of SNTG1

The PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif of RSK1. Determined by X-ray diffraction at 2.5 Å resolution. Released 20 Apr 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,914
Mol. weight: 96.88 kDa
Ligands: CA
Released: 20 Apr 2022

Explore 7PC8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PC8 contains 49 α-helices and 18 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: 26 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	51-52	2	1
α-helix	53-55	3
β-strand	56-61	6	2
β-strand	63	1	3
β-strand	67	1	3
β-strand	70-75	6	2
α-helix	76-78	3
β-strand	80-87	8	2
α-helix	89-94	6
β-strand	103-108	6	2
β-strand	111-112	2	2
α-helix	118-126	9
β-strand	131-138	8	2
β-strand	139-140	2	1
α-helix	141-143	3
α-helix	158-170	13
α-helix	176-183	8
α-helix	188-202	15
α-helix	206-213	8
α-helix	216-226	11
α-helix	229-240	12
α-helix	248-257	10
α-helix	260-274	15
α-helix	278-285	8
α-helix	288-298	11
α-helix	302-306	5
α-helix	311-324	14
α-helix	333-342	10
α-helix	345-358	14
α-helix	363-370	8
α-helix	373-387	15
α-helix	389-402	14
α-helix	408-417	10
α-helix	423-434	12
α-helix	438-445	8
α-helix	448-458	11

Chain B: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	55-61	7	4
β-strand	70-75	6	4
α-helix	76-78	3
β-strand	80-87	8	4
α-helix	89-95	7
β-strand	103-108	6	4
β-strand	111-112	2	4
α-helix	118-126	9
β-strand	131-138	8	4
α-helix	158-170	13
α-helix	176-183	8
α-helix	188-202	15
α-helix	206-213	8
α-helix	216-226	11
α-helix	229-240	12
α-helix	248-257	10
α-helix	260-274	15
α-helix	278-285	8
α-helix	288-298	11
α-helix	302-304	3
α-helix	311-323	13
α-helix	333-342	10
α-helix	345-358	14
α-helix	363-370	8
α-helix	373-401	29
α-helix	408-417	10
α-helix	423-434	12
α-helix	438-445	8
α-helix	448-458	11

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	186-188	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-1-syntrophin,Annexin A2	A, B	protein	414	Homo sapiens	P07355 (AlphaFold model), Q9NSN8 (AlphaFold model)
Ribosomal protein S6 kinase alpha-1	C, D	protein	10	Homo sapiens	Q15418 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7PC8_1 Gamma-1-syntrophin,Annexin A2 (chains A, B)
GSHMGGERTVTIRRQTVGGFGLSIKGGAEHNIPVVVSKISKEQRAELSGLLFIGDAILQI
NGINVRKCRHEEVVQVLRNAGEEVTLTVSFLKRAPGSAYGSVKAYTNFDAERDALNIETA
IKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKT
PAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSG
DFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHL
QKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRD
KVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD

Sequence of entity 2 (C, D), FASTA

>7PC8_2 Ribosomal protein S6 kinase alpha-1 (chains C, D)
RVRKLPETTL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	9

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

Primary citation

A scalable strategy to solve structures of PDZ domains and their complexes. Cousido-Siah, A., Carneiro, L., Kostmann, C. et al. Acta Crystallogr D Struct Biol (2022) 78:509-516. DOI 10.1107/S2059798322001784 · PubMed

Other PDB entries of the same protein (UniProt P07355 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HYV 1.42 Å, Human Annexin A2 with heparin hexasaccharide bound
1W7B 1.52 Å, Annexin A2: Does it induce membrane aggregation by a new multimeric state of the protein.
7QQM 1.6 Å, The PDZ domain of LRRC7 fused with ANXA2
7PC5 1.7 Å, The third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4
7P73 1.85 Å, The PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1
2HYU 1.86 Å, Human Annexin A2 with heparin tetrasaccharide bound
7ZVN 1.87 Å, Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10…
5LPX 1.9 Å, Crystal structure of PKC phosphorylation-mimicking mutant (S26E) Annexin A2
7P74 1.9 Å, The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1
7PC3 1.95 Å, The second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1
7P70 2.0 Å, The PDZ-domain of SNTB1 complexed with the PDZ-binding motif of HPV35-E6
7PCB 2.0 Å, The PDZ domain of SNX27 fused with ANXA2

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