SMTL ID : 7oxh.1

ttSlyD with pseudo-wild-type S2 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x UNK- UNK: Fragment of 30S ribosomal protein S2 peptide(Non-functional Binders)

UNK-UNK.1: 4 residues within 4Å: Chain A: G.70, Q.72, F.117 Ligands: PE4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.72

3 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.2: 7 residues within 4Å: Chain A: Q.72, Q.94, D.95, M.96, M.101, F.117 Ligands: UNK-UNK.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.72, A:Q.72, A:D.95, A:M.96 PE4.3: 4 residues within 4Å: Chain A: M.1, E.48, E.49, V.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1, A:E.49 Water bridges: A:G.50 PE4.5: 6 residues within 4Å: Chain A: V.17, E.18, H.66, A.122, G.123, K.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.124

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: R.12, Y.13, T.14, Q.129, E.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.14

2 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.6: 1 residues within 4Å: Chain A: E.97 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.97, H2O.2 NI.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.8: 6 residues within 4Å: Chain A: Y.29, L.30, N.35, H.147, A.148, S.151 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pazicky, S. et al., Impact of distant peptide substrate residues on enzymatic activity of SlyD. Cell.Mol.Life Sci. (2022)

Release Date

2022-03-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidyl-prolyl cis-trans isomerase

30S ribosomal protein S2

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