4ODQ: SlyD delta-IF from Thermus thermophilus

Structure of SlyD delta-IF from Thermus thermophilus in complex with S3 peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Thermus thermophilus, Homo sapiens, Escherichia coli
Chains: 2
Atoms: 1,005
Mol. weight: 14.22 kDa
Ligands: NI, CA
Released: 14 Jan 2015

Explore 4ODQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ODQ contains 6 α-helices and 6 β-strands across 1 chain. 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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	7-17	11	2
β-strand	20-30	11	2
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	76-77	2
β-strand	78-89	12	2
α-helix	90-91	2
α-helix	92-97	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera	A	protein	110	Thermus thermophilus, Homo sapiens	P62942 (AlphaFold model), Q5SLE7 (AlphaFold model)
30S ribosomal protein S3	B	protein	16	Escherichia coli	P0A7V3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ODQ_1 Peptidyl-prolyl cis-trans isomerase SlyD, Peptidyl-prolyl cis-trans isomerase FKBP1A chimera (chains A)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGATGHPGIIPPHATLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

Sequence of entity 2 (B), FASTA

>4ODQ_2 30S ribosomal protein S3 (chains B)
RLGIVKPWNSTWFANX

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1
CA	Calcium ion	Ca	4

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

Primary citation

Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. Quistgaard, E.M., Weininger, U., Ural-Blimke, Y. et al. BMC Biol (2016) 14:82-82. DOI 10.1186/s12915-016-0300-3 · PubMed

Other PDB entries of the same protein (UniProt P62942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PPN 0.92 Å, Crystal structure of FKBP12
2PPP 0.94 Å, Crystal structure of E60Q mutant of FKBP12
6YF3 1.0 Å, FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
6YF2 1.03 Å, FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
8X6P 1.05 Å, Isomerase Protein
6YF1 1.12 Å, FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution
8CHM 1.12 Å, Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-…
4N19 1.2 Å, Structural basis of conformational transitions in the active site and 80 s loop in the…
8PDF 1.2 Å, FKBP12 in complex with PROTAC 6a2
9LYG 1.26 Å, Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
2PPO 1.29 Å, Crystal structure of E60A mutant of FKBP12
7U8D 1.39 Å, FKBP12 mutant V55G bound to Rapa*-3Z

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