SMTL ID : 8r5v.1

Crystal structure of bovine pancreatic ribonuclease A in complex with [Sp-PS]-mU-dT dinucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x Y4I: 1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione(Non-covalent)

Y4I.1: 11 residues within 4Å: Chain A: Q.37, H.38, K.67, V.69, N.70, T.71, K.92, H.145, F.146, D.147 Ligands: TF4.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.67, A:T.71, A:T.71, A:T.71, A:K.92, A:K.92 Water bridges: A:Q.37, A:Q.37, A:K.67, A:H.145, A:S.149, A:S.149

2 x TF4: DICHLORO-ACETIC ACID(Non-covalent)

TF4.2: 8 residues within 4Å: Chain A: K.33, F.34, Q.37, H.38, V.144, H.145, F.146 Ligands: Y4I.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.146 Salt bridges: A:H.38, A:K.67, A:H.145 TF4.3: 6 residues within 4Å: Chain B: H.38, K.67, V.69, N.70, T.71, F.146 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.71 Water bridges: B:K.67 Salt bridges: B:H.38, B:K.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jastrzebska, K. et al., P-Stereodefined morpholino dinucleoside 3',5'-phosphorothioates. Org.Biomol.Chem. (2024)

Release Date

2023-12-06

Peptides

Ribonuclease pancreatic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease pancreatic