4ODL: SlyD from Thermus thermophilus

Structure of SlyD from Thermus thermophilus in complex with S2 peptide. Determined by X-ray diffraction at 2.92 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 2.92 Å
Organisms: Thermus thermophilus, Escherichia coli
Chains: 6
Atoms: 2,791
Mol. weight: 42.3 kDa
Released: 14 Jan 2015

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

Secondary structure: helices and β-sheets

4ODL contains 16 α-helices and 25 β-strands across 6 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	1
β-strand	20-30	11	1
β-strand	36	1	2
α-helix	38-44	7
α-helix	47-48	2
β-strand	52-57	6	1
α-helix	59-61	3
α-helix	68-70	3
β-strand	71-75	5	3
α-helix	76-78	3
β-strand	90-94	5	3
β-strand	101-109	9	3
β-strand	112-116	5	3
α-helix	124-125	2
β-strand	126-137	12	1
α-helix	138-139	2
α-helix	140-145	6

Chain B: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	4
β-strand	7-17	11	5
β-strand	20-30	11	5
β-strand	36	1	6
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	4
β-strand	52-57	6	5
α-helix	59-61	3
α-helix	68-70	3
β-strand	71-75	5	7
α-helix	76-78	3
α-helix	80	1
β-strand	90-94	5	7
β-strand	100-109	10	7
β-strand	112-116	5	7
β-strand	126-137	12	5
α-helix	138-139	2
α-helix	140-145	6

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	7
β-strand	31	1	7

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	30-32	3	3

Chains E and F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	28	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase SlyD	A, B	protein	158	Thermus thermophilus	Q5SLE7 (AlphaFold model)
30S ribosomal protein S2	C, D, E, F	protein	16	Escherichia coli	P0A7V0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ODL_1 Peptidyl-prolyl cis-trans isomerase SlyD (chains A, B)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHP
LAGKDLDFQVEVVKVREATPEELLHGHAHPSGHHHHHH

Sequence of entity 2 (C, D, E, F), FASTA

>4ODL_2 30S ribosomal protein S2 (chains C, D, E, F)
TRYWNPKMKPFIFGAX

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
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
3CGM 2.41 Å, Crystal structure of thermophilic SlyD
3LUO 2.55 Å, Crystal Structure and functional characterization of the thermophilic prolyl isomerase…

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