4ODM: SlyD from Thermus thermophilus

Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide. Determined by X-ray diffraction at 1.75 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Thermus thermophilus, Escherichia coli
Chains: 13
Atoms: 6,039
Mol. weight: 83.14 kDa
Released: 14 Jan 2015

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

Secondary structure: helices and β-sheets

4ODM contains 40 α-helices and 52 β-strands across 12 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.

Chains A and B: 8 helices, 11 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	65-67	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

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
β-strand	7-17	11	10
β-strand	20-30	11	10
β-strand	36	1	11
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	9
β-strand	52-57	6	10
α-helix	59-61	3
α-helix	65-67	3
α-helix	68-70	3
β-strand	71-75	5	12
α-helix	76-78	3
β-strand	90-94	5	12
β-strand	100-109	10	12
β-strand	112-116	5	12
β-strand	126-137	12	10
α-helix	138-139	2
α-helix	140-145	6
α-helix	148-150	3

Chain D: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	13
β-strand	7-17	11	14
β-strand	20-30	11	14
β-strand	36	1	15
α-helix	38-44	7
α-helix	47	1
β-strand	48	1	13
β-strand	52-57	6	14
α-helix	59-61	3
α-helix	65-67	3
α-helix	68-70	3
β-strand	71-75	5	16
α-helix	76-78	3
α-helix	80	1
β-strand	90-94	5	16
β-strand	100-109	10	16
β-strand	112-116	5	16
β-strand	126-137	12	14
α-helix	138-139	2
α-helix	140-145	6

Chains E, G and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	28	1	3

Chains F and J: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	32	1	4

Chains H and L: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	32-33	2	8

Chain K: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	27	1
β-strand	28	1	15
α-helix	30	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase SlyD	A, B, C, D	protein	153	Thermus thermophilus	Q5SLE7 (AlphaFold model)
30S ribosomal protein S2	E, F, G, H, I, J, K, L, M	protein	16	Escherichia coli	P0A7V0 (AlphaFold model)

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

>4ODM_1 Peptidyl-prolyl cis-trans isomerase SlyD (chains A, B, C, D)
MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAE
KAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHP
LAGKDLDFQVEVVKVREATPEELLHGHAHLVPK

Sequence of entity 2 (E, F, G, H, I, J, K, L, M), FASTA

>4ODM_2 30S ribosomal protein S2 (chains E, F, G, H, I, J, K, L, M)
TRYANPKMKPFIFGAX

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
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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