5X3F: YgjG-Protein A-Zpa963-PKA catalytic domain

Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain. Determined by X-ray diffraction at 3.38 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 3.38 Å
Organisms: Escherichia coli (strain K12), Staphylococcus aureus, Mus musculus
Chains: 2
Atoms: 6,616
Mol. weight: 99.93 kDa
Released: 28 Jun 2017

Explore 5X3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X3F contains 46 α-helices and 31 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: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	50-53	4
α-helix	55-58	4
β-strand	67-70	4	1
β-strand	75-78	4	1
β-strand	83-86	4	1
α-helix	89-92	4
α-helix	101-113	13
α-helix	124-136	13
β-strand	141-147	7	2
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-177	6	2
α-helix	187-189	3
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-211	5	2
α-helix	215-227	13
β-strand	232-237	6	2
β-strand	241	1	3
β-strand	247	1	3
α-helix	248-250	3
α-helix	253-263	11
β-strand	267-271	5	2
β-strand	276	1	4
β-strand	284	1	4
α-helix	285-287	3
β-strand	295-298	4	2
α-helix	300-303	4
β-strand	310-315	6	2
α-helix	316-319	4
α-helix	320-323	4
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	5
β-strand	389-395	7	5
α-helix	398-410	13
β-strand	413-414	2	1
β-strand	424-427	4	5
α-helix	435-462	28
α-helix	469-481	13
α-helix	483-486	4
α-helix	488-497	10

Chain B: 19 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	124-136	13
α-helix	141-170	30
α-helix	179-181	3
β-strand	182-190	9	6
β-strand	194-201	8	6
β-strand	207-214	8	6
α-helix	215-221	7
α-helix	224-236	13
β-strand	242	1	7
β-strand	245-250	6	6
β-strand	254-260	7	6
β-strand	266	1	7
α-helix	267-274	8
α-helix	279-298	20
β-strand	301-302	2	8
α-helix	308-310	3
β-strand	311-313	3	7
β-strand	319-321	3	7
β-strand	328-329	2	8
β-strand	334	1	9
α-helix	341-343	3
α-helix	346-350	5
β-strand	354	1	9
α-helix	357-372	16
α-helix	383-390	8
α-helix	395-397	3
α-helix	402-411	10
α-helix	428-431	4
α-helix	434-436	3
α-helix	441-446	6
α-helix	450-451	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putrescine aminotransferase,Immunoglobulin G-binding protein A	A	protein	501	Escherichia coli (strain K12), Staphylococcus aureus	P38507 (AlphaFold model), P42588 (AlphaFold model)
Zpa963,cAMP-dependent protein kinase catalytic subunit alpha	B	protein	393	Staphylococcus aureus, Mus musculus	P05132 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5X3F_1 Putrescine aminotransferase,Immunoglobulin G-binding protein A (chains A)
GSHMSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGD
YGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL
DPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHG
KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG
EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL
GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK
GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA
KTIRIEPPLTLTIEQCELVIKAARKALAAMRQQVAFYEILHLPNLNEEQRNAFIQSLKDD
PSQSANLLAEAKKLNDAQAPK

Sequence of entity 2 (B), FASTA

>5X3F_2 Zpa963,cAMP-dependent protein kinase catalytic subunit alpha (chains B)
GSHMVDNKFNKETQEASWEIFTLPNLNGRQVAAFISSLLDDPSQSANLLAEAKKLNDVQA
FLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQ
KVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGR
FSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWT
LCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRF
PSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPK
FKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF

Primary citation

Construction of novel repeat proteins with rigid and predictable structures using a shared helix method. Youn, S.J., Kwon, N.Y., Lee, J.H. et al. Sci Rep (2017) 7:2595-2595. DOI 10.1038/s41598-017-02803-z · PubMed

Other PDB entries of the same protein (UniProt P38507 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NPD 0.9 Å, High-resolution structure of C domain of staphylococcal protein A at cryogenic temperature
4NPE 1.42 Å, High-resolution structure of C domain of staphylococcal protein A at room temperature
4NPF 1.49 Å, High-resolution structure of two tandem B domains of staphylococcal protein A connected…
8CPL 1.6 Å, YZw2 a scaffold for cryo-EM of small proteins of interest
4ZMD 1.87 Å, C domain of staphylococcal protein A mutant - Q9W
4ZNC 2.28 Å, Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant…
1LP1 2.3 Å, Protein Z in complex with an in vitro selected affibody
5CBN 2.3 Å, Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus with…
4WWI 2.31 Å, Crystal structure of the C domain of staphylococcal protein A in complex with the Fc…
5H7D 2.57 Å, Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex
5EWX 2.6 Å, Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with…
5H76 2.6 Å, Crystal structure of the DARPin-Protein A fusion protein

Browse structure collections

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