SMTL ID : 5ogh.1

Structure of RNase A at high resolution (1.16 A) in complex with 3'-CMP and sulphate ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

2 x C3P: CYTIDINE-3'-MONOPHOSPHATE(Non-covalent)

C3P.1: 11 residues within 4Å: Chain A: Q.11, H.12, K.41, V.43, N.44, T.45, K.66, H.119, F.120, A.122, S.123 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:H.12, A:K.41, A:N.44, A:T.45, A:T.45, A:T.45, A:F.120 Water bridges: A:V.118, A:H.119, A:S.123, A:S.123 Salt bridges: A:H.12, A:H.119 C3P.2: 6 residues within 4Å: Chain A: K.1, E.2, R.10, N.34, L.35, K.37 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.1, A:E.2, A:E.2, A:R.10, A:R.10, A:N.34 Water bridges: A:K.7, A:R.10 pi-Cation interactions: A:R.10

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

SO4.3: 2 residues within 4Å: Chain A: S.22, S.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.23, A:S.23, A:S.23

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

CL.4: 1 residues within 4Å: Chain A: K.61 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: S.15, S.50 Ligands: NA.9 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: S.50, L.51, A.52 Ligands: NA.9 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: Q.55, A.56, C.58, S.59 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.74, S.75, H.105 Ligand excluded by PLIP

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

NA.9: 5 residues within 4Å: Chain A: S.15, S.50, L.51 Ligands: CL.5, CL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.15, A:L.51 NA.10: 3 residues within 4Å: Chain A: K.31, S.32, N.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.34, A:N.34 Water bridges: A:K.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prats-Ejarque, G. et al., Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates. Biochim Biophys Acta Gen Subj (2019)

Release Date

2018-08-01

Peptides

Ribonuclease pancreatic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease pancreatic

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