SMTL ID : 4odn.1

Structure of SlyD from Thermus thermophilus in complex with S2-plus peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-oligomer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: S.28, Y.29, L.30, N.35, H.147, A.148 Ligands: NA.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.30, A:A.148 Water bridges: A:N.35 Salt bridges: A:H.147 SO4.2: 3 residues within 4Å: Chain A: R.47, F.53, Q.54 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.47, A:R.47, A:Q.54, A:Q.54 Salt bridges: A:R.47 SO4.8: 5 residues within 4Å: Chain B: F.5, I.6, F.7, G.8, K.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.6, B:F.7, B:G.8 Salt bridges: B:K.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: E.42, A.43, E.45, G.46, R.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.42, A:G.46, A:R.47 Water bridges: A:E.42 GOL.4: 6 residues within 4Å: Chain A: L.27, I.37, L.40, Y.63, F.128 Ligands: CL.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.13

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: L.36, I.37 Ligands: GOL.4 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.107, E.109, E.112, T.114 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 4 residues within 4Å: Chain A: Y.29, L.30, N.35 Ligands: SO4.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.30, A:N.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quistgaard, E.M. et al., Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD. BMC Biol. (2016)

Release Date

2015-01-14

Peptides

Peptidyl-prolyl cis-trans isomerase SlyD: A
30S ribosomal protein S2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidyl-prolyl cis-trans isomerase SlyD

30S ribosomal protein S2

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