5H7D: YgjG-protein A-Zpa963-calmodulin complex

Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex. Determined by X-ray diffraction at 2.57 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 2.57 Å
Organisms: Escherichia coli (strain K12), Staphylococcus aureus, synthetic construct
Chains: 16
Atoms: 37,132
Mol. weight: 540.49 kDa
Ligands: CA
Released: 28 Jun 2017

Explore 5H7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5H7D contains 280 α-helices and 168 β-strands across 16 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.

Chains A, C, I and M: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-64	5
β-strand	66	1	1
β-strand	67-70	4	2
β-strand	75-78	4	2
β-strand	83-86	4	2
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	3
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	4
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	4
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	4
α-helix	215-227	13
β-strand	232-237	6	4
β-strand	241	1	5
β-strand	247	1	5
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	4
α-helix	285-288	4
β-strand	295-298	4	4
α-helix	300-303	4
β-strand	310-315	6	4
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	6
β-strand	390-395	6	6
α-helix	398-410	13
β-strand	413-414	2	2
β-strand	416-418	3	6
β-strand	421-427	7	6
α-helix	435-463	29
α-helix	469-481	13
α-helix	483-485	3
α-helix	486-498	13

Chains B and J: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-64	5
β-strand	66	1	3
β-strand	67-70	4	7
β-strand	75-78	4	7
β-strand	83-86	4	7
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	1
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	8
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	8
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	8
α-helix	215-227	13
β-strand	232-237	6	8
β-strand	241	1	9
β-strand	247	1	9
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	8
α-helix	285-288	4
β-strand	295-298	4	8
α-helix	300-303	4
β-strand	310-315	6	8
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	10
β-strand	390-395	6	10
α-helix	398-410	13
β-strand	413-414	2	7
β-strand	416-418	3	10
β-strand	421-427	7	10
α-helix	435-463	29
α-helix	471-481	11
α-helix	487-497	11

Chain D: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-64	5
β-strand	66	1	15
β-strand	67-70	4	19
β-strand	75-78	4	19
β-strand	83-86	4	19
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	13
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	20
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	20
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	20
α-helix	215-227	13
β-strand	232-237	6	20
β-strand	241	1	21
β-strand	247	1	21
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	20
α-helix	285-288	4
β-strand	295-298	4	20
α-helix	300-303	4
β-strand	310-315	6	20
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	22
β-strand	390-395	6	22
α-helix	398-410	13
β-strand	413-414	2	19
β-strand	416-418	3	22
β-strand	421-427	7	22
α-helix	435-463	29
α-helix	469-481	13
α-helix	487-497	11

Chains E, G, K and O: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	124-136	13
α-helix	138-140	3
α-helix	141-164	24
β-strand	172	1	11
α-helix	174-183	10
α-helix	190-200	11
β-strand	208	1	11
α-helix	210-218	9

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	124-136	13
α-helix	142-162	21
β-strand	172	1	12
α-helix	174-183	10
α-helix	190-200	11
β-strand	208	1	12
α-helix	210-217	8

Chains H, L and P: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	108-117	10
α-helix	124-136	13
α-helix	142-164	23
β-strand	172	1	24
α-helix	174-183	10
α-helix	190-200	11
β-strand	208	1	24
α-helix	210-217	8

Chain N: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	28-41	14
α-helix	42-46	5
α-helix	48-56	9
α-helix	60-64	5
β-strand	66	1	39
β-strand	67-70	4	43
β-strand	75-78	4	43
β-strand	83-86	4	43
α-helix	89-92	4
α-helix	101-113	13
β-strand	122	1	37
α-helix	123	1
α-helix	124-136	13
β-strand	141-147	7	44
α-helix	150-165	16
α-helix	166-168	3
β-strand	172-176	5	44
α-helix	185-190	6
α-helix	194-197	4
α-helix	198-200	3
β-strand	207-210	4	44
α-helix	215-227	13
β-strand	232-237	6	44
β-strand	241	1	45
β-strand	247	1	45
α-helix	248-250	3
α-helix	253-264	12
α-helix	266	1
β-strand	267-271	5	44
α-helix	285-288	4
β-strand	295-298	4	44
α-helix	300-303	4
β-strand	310-315	6	44
α-helix	316-319	4
α-helix	320-322	3
α-helix	337-352	16
α-helix	355-376	22
β-strand	381-387	7	46
β-strand	390-395	6	46
α-helix	398-410	13
β-strand	413-414	2	43
β-strand	416-418	3	46
β-strand	421-427	7	46
α-helix	435-462	28
α-helix	469-481	13
α-helix	487-499	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Putrescine aminotransferase,Immunoglobulin G-binding protein A	A, B, C, D, I, J, M, N	protein	499	Escherichia coli (strain K12), Staphylococcus aureus	P38507 (AlphaFold model), P42588 (AlphaFold model)
Zpa963,Calmodulin	E, F, G, H, K, L, O, P	protein	120	synthetic construct, Caenorhabditis elegans	O16305 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, I, J, M, N), FASTA

>5H7D_1 Putrescine aminotransferase,Immunoglobulin G-binding protein A (chains A, B, C, D, I, J, M, N)
GSHMSASALACSAHALNLIEKRTLDHEEMKALNREVIEYFKEHVNPGFLEYRKSVTAGGD
YGAVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELL
DPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHG
KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG
EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL
GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK
GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA
KTIRIEPPLTLTIEQCELVIKAARKALAAMRQQVAFYEILHLPNLNEEQRNAFIQSLKDD
PSQSANLLAEAKKLNDAQA

Sequence of entity 2 (E, F, G, H, K, L, O, P), FASTA

>5H7D_2 Zpa963,Calmodulin (chains E, F, G, H, K, L, O, P)
GSHMKFNKETQEASWEIFTLPNLNGRQVAAFISSLLDDPSQSANLLAEAKKLNQIQAFKE
AFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	16

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…
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
5H79 2.7 Å, Crystal structure of a repeat protein with three Protein A repeat module

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