5N7D: MAGI-1

MAGI-1 complexed with a RSK1 peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,750
Mol. weight: 102.2 kDa
Ligands: CA
Released: 8 Nov 2017

Explore 5N7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N7D contains 49 α-helices and 17 β-strands across 3 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
α-helix	463-465	3
β-strand	469-476	8	1
β-strand	478	1	2
β-strand	481	1	2
β-strand	484-487	4	1
β-strand	497-501	5	1
α-helix	506-510	5
β-strand	518-522	5	1
β-strand	525-526	2	1
α-helix	532-541	10
α-helix	543	1
β-strand	547-554	8	1
α-helix	574-586	13
α-helix	592-599	8
α-helix	604-618	15
α-helix	622-629	8
α-helix	632-642	11
α-helix	645-656	12
α-helix	664-673	10
α-helix	676-690	15
α-helix	694-701	8
α-helix	704-714	11
α-helix	718-722	5
α-helix	727-740	14
α-helix	749-758	10
α-helix	761-774	14
α-helix	779-786	8
α-helix	789-818	30
α-helix	824-834	11
α-helix	839-850	12
α-helix	854-861	8
α-helix	864-874	11

Chain B: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	469	1
β-strand	470-476	7	3
β-strand	484	1	4
β-strand	497	1	5
β-strand	501	1	4
α-helix	506-509	4
β-strand	518	1	5
β-strand	521-522	2	3
β-strand	526	1	3
α-helix	536-541	6
α-helix	543	1
β-strand	547-553	7	3
α-helix	567-569	3
α-helix	574-585	12
α-helix	592-599	8
α-helix	604-618	15
α-helix	622-627	6
α-helix	632-642	11
α-helix	645-657	13
α-helix	665-673	9
α-helix	676-690	15
α-helix	694-701	8
α-helix	704-714	11
α-helix	718-720	3
α-helix	727-740	14
α-helix	749-758	10
α-helix	761-774	14
α-helix	779-786	8
α-helix	789-818	30
α-helix	824-834	11
α-helix	839-850	12
α-helix	854-861	8
α-helix	865-874	10

Chain C: 0 helices, 1 β-strand

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2	A, B	protein	427	Homo sapiens	P07355 (AlphaFold model), Q96QZ7 (AlphaFold model)
Ribosomal protein S6 kinase alpha-1	C	protein	49	Homo sapiens	Q15418 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5N7D_1 Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2 (chains A, B)
GSMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDG
KMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYPLGSSAYGSVKAYTN
FDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALS
GHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYK
TDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPK
WISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFAD
RLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALL
YLCGGDD

Sequence of entity 2 (C), FASTA

>5N7D_2 Ribosomal protein S6 kinase alpha-1 (chains C)
GSQDLQLVKGAMAATYSALNSSKPTPQLKPIESSILAQRRVRKLPSTTL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7

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

Primary citation

Dynamic control of RSK complexes by phosphoswitch-based regulation. Gogl, G., Biri-Kovacs, B., Poti, A.L. et al. FEBS J (2018) 285:46-71. DOI 10.1111/febs.14311 · 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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