4ODO: SlyD from Thermus thermophilus

Structure of SlyD from Thermus thermophilus in complex with FK506. Determined by X-ray diffraction at 1.6 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Thermus thermophilus
Chains: 3
Atoms: 4,385
Mol. weight: 55.12 kDa
Ligands: MG, FK5, BTB
Released: 14 Jan 2015

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

Secondary structure: helices and β-sheets

4ODO contains 26 α-helices and 32 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: 8 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
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	65-67	3
α-helix	68-70	3
β-strand	71-75	5	3
α-helix	76-78	3
β-strand	90-91	2	3
β-strand	94	1	4
β-strand	100	1	4
β-strand	103-109	7	3
β-strand	112-116	5	3
β-strand	126-137	12	2
α-helix	138-139	2
α-helix	140-145	6

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	7-17	11	6
β-strand	20-30	11	6
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	5
β-strand	52-57	6	6
α-helix	59-61	3
α-helix	65-67	3
α-helix	68-70	3
β-strand	71-75	5	7
α-helix	76-78	3
β-strand	90-94	5	7
β-strand	100-109	10	7
β-strand	112-116	5	7
α-helix	124-125	2
β-strand	126-137	12	6
α-helix	138-139	2
α-helix	140-145	6

Chain C: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	8
β-strand	7-17	11	9
β-strand	20-30	11	9
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	8
β-strand	52-57	6	9
α-helix	59-61	3
α-helix	65-67	3
α-helix	68-70	3
β-strand	71-75	5	10
α-helix	76-78	3
β-strand	90-94	5	10
β-strand	100-109	10	10
β-strand	112-116	5	10
β-strand	126-137	12	9
α-helix	138-139	2
α-helix	140-145	6
α-helix	148-150	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase SlyD	A, B, C	protein	158	Thermus thermophilus	Q5SLE7 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>4ODO_1 Peptidyl-prolyl cis-trans isomerase SlyD (chains A, B, C)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHP
LAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
FK5	8-deethyl-8-[but-3-enyl]-ascomycin	C44 H69 N O12	3
BTB	2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol	C8 H19 N O5	1

Water and common crystallization additives (CL, GOL) 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 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
7OXH 1.7 Å, ttSlyD with pseudo-wild-type S2 peptide
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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