3CGM: Thermophilic SlyD

Crystal structure of thermophilic SlyD. Determined by X-ray diffraction at 2.41 Å resolution. Released 10 Mar 2009.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Thermus thermophilus
Chains: 1
Atoms: 1,382
Mol. weight: 17.99 kDa
Ligands: NI, SCN
Released: 10 Mar 2009

Explore 3CGM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CGM contains 7 α-helices and 10 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: 7 helices, 10 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	68-70	3
β-strand	71-75	5	3
α-helix	76-78	3
β-strand	90-95	6	3
β-strand	99-109	11	3
β-strand	112-116	5	3
β-strand	126-137	12	2
α-helix	138-139	2
α-helix	140-145	6

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>3CGM_1 Peptidyl-prolyl cis-trans isomerase (chains A)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHP
LAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	1
SCN	Thiocyanate ion	C N S	6

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

Primary citation

Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus. Loew, C., Neumann, P., Tidow, H. et al. J Mol Biol (2010) 398:375-390. DOI 10.1016/j.jmb.2010.03.014 · 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
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
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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