7P74: The PDZ domain of SYNJ2BP

The PDZ domain of SYNJ2BP complexed with the phosphorylated PDZ-binding motif of RSK1. Determined by X-ray diffraction at 1.9 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,675
Mol. weight: 49.82 kDa
Ligands: CA
Released: 27 Jul 2022

Explore 7P74 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P74 contains 24 α-helices and 9 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: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	1
β-strand	19	1	2
β-strand	22	1	2
β-strand	25-29	5	1
β-strand	42-47	6	1
α-helix	52-56	5
β-strand	64-68	5	1
β-strand	71-72	2	1
α-helix	78-86	9
β-strand	91-101	11	1
α-helix	118-130	13
α-helix	136-143	8
α-helix	148-162	15
α-helix	166-173	8
α-helix	176-186	11
α-helix	189-200	12
α-helix	203-205	3
α-helix	208-217	10
α-helix	220-234	15
α-helix	238-245	8
α-helix	248-258	11
α-helix	262-266	5
α-helix	271-284	14
α-helix	293-302	10
α-helix	305-318	14
α-helix	323-330	8
α-helix	333-347	15
α-helix	349-361	13
α-helix	368-378	11
α-helix	383-394	12
α-helix	398-405	8
α-helix	408-418	11

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	733-734	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptojanin-2-binding protein,Annexin A2	A	protein	421	Homo sapiens	P07355 (AlphaFold model), P57105 (AlphaFold model)
Ribosomal protein S6 kinase alpha-1	B	protein	15	Homo sapiens	Q15418 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7P74_1 Synaptojanin-2-binding protein,Annexin A2 (chains A)
GSHMDYLVTEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQE
GDKILSVNGQDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQGSAYGSVKAYTNFDAERD
ALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETV
ILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKD
IISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMT
ERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSM
KGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGD
D

Sequence of entity 2 (B), FASTA

>7P74_2 Ribosomal protein S6 kinase alpha-1 (chains B)
TDDSRRVRKLPSTTL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

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

Primary citation

Quantitative fragmentomics allow affinity mapping of interactomes. Gogl, G., Zambo, B., Kostmann, C. et al. Nat Commun (2022) 13:5472-5472. DOI 10.1038/s41467-022-33018-0 · 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
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
2HYW 2.1 Å, Human Annexin A2 with Calcium bound

Browse structure collections

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