7OXH: TtSlyD with pseudo-wild-type S2 peptide

ttSlyD with pseudo-wild-type S2 peptide. Determined by X-ray diffraction at 1.7 Å resolution. Released 16 Mar 2022.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8), Escherichia coli (strain K12), synthetic construct
Chains: 3
Atoms: 1,413
Mol. weight: 20.69 kDa
Ligands: PE4, NI
Released: 16 Mar 2022

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

Secondary structure: helices and β-sheets

7OXH contains 7 α-helices and 13 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: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-17	11	2
β-strand	20-30	11	2
β-strand	36	1	3
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	1
β-strand	52-57	6	2
α-helix	59-61	3
α-helix	68-70	3
β-strand	71-75	5	4
α-helix	76-78	3
β-strand	90-94	5	4
β-strand	100-109	10	4
β-strand	112-116	5	4
β-strand	126-137	12	2
α-helix	138-139	2
α-helix	140-145	6
β-strand	152-153	2	2

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase	A	protein	158	Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)	Q5SLE7 (AlphaFold model)
30S ribosomal protein S2	B	protein	15	Escherichia coli (strain K12)	P0A7V0 (AlphaFold model)
Fragment of 30S ribosomal protein S2 peptide	E	protein	2	synthetic construct

Sequence of entity 1 (A), FASTA

>7OXH_1 Peptidyl-prolyl cis-trans isomerase (chains A)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHP
LAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

Sequence of entity 2 (B), FASTA

>7OXH_2 30S ribosomal protein S2 (chains B)
TRYWNAKMLPFAFGA

Sequence of entity 3 (E), FASTA

>7OXH_3 Fragment of 30S ribosomal protein S2 peptide (chains E)
XX

Ligands and cofactors

ID	Name	Formula	Copies
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	3
NI	Nickel (II) ion	Ni	2

Water and common crystallization additives (PEG, CL) are not listed.

Primary citation

Impact of distant peptide substrate residues on enzymatic activity of SlyD. Pazicky, S., Werle, A.A., Lei, J. et al. Cell Mol Life Sci (2022) 79:138-138. DOI 10.1007/s00018-022-04179-4 · PubMed

Other PDB entries of the same protein (UniProt Q5SLE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ODK 1.4 Å, Structure of SlyD from Thermus thermophilus in complex with T1 peptide
4ODN 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide
4ODO 1.6 Å, Structure of SlyD from Thermus thermophilus in complex with FK506
4ODP 1.75 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S2-W23A peptide
4ODM 1.75 Å, Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide
7OXJ 1.85 Å, ttSlyD with M8A pseudo-wild-type S2 peptide
4ODR 1.93 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506
4ODQ 2.0 Å, Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide
7OXG 2.0 Å, ttSlyD FKBP domain with M8A pseudo-wild-type S2 peptide
3CGM 2.41 Å, Crystal structure of thermophilic SlyD
3LUO 2.55 Å, Crystal Structure and functional characterization of the thermophilic prolyl isomerase…
7OXI 2.6 Å, ttSlyD with W4A pseudo-wild-type S2 peptide

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