SMTL ID : 7oxj.1

ttSlyD with M8A pseudo-wild-type S2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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: 7 residues within 4Å: Chain A: D.67, G.70, Q.72, M.101, F.117, N.118 Ligands: PG4.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.117

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 1 residues within 4Å: Chain A: E.97 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.97, H2O.1, H2O.2

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 4 residues within 4Å: Chain A: M.1, E.48, E.49 Ligands: PGE.5 No protein-ligand interaction detected (PLIP) PGE.5: 4 residues within 4Å: Chain A: G.50, A.52, E.131 Ligands: PGE.3 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 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

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.7: 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
D

Peptidyl-prolyl cis-trans isomerase

30S ribosomal protein S2

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