SMTL ID : 6enp.1

Atomic resolution structure of human RNase 6 in the presence of phosphate anions in P21 space group.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: H.37, K.39, H.40 7 PLIP interactions: 7 interactions with chain A Water bridges: A:H.37, A:K.39, A:K.39, A:K.39, A:H.40 Salt bridges: A:H.37, A:K.39 PO4.2: 3 residues within 4Å: Chain A: Q.111, K.112, S.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.111, A:K.112 Water bridges: A:K.112, A:S.113 Salt bridges: A:K.112 PO4.3: 1 residues within 4Å: Chain A: R.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.26 Salt bridges: A:R.26

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 1 residues within 4Å: Chain A: H.40 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.40, H2O.8

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

NA.5: 1 residues within 4Å: Chain A: R.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.5 NA.6: 5 residues within 4Å: Chain A: P.19, H.46, D.47, S.48 Ligands: CL.8 No protein-ligand interaction detected (PLIP) NA.7: 3 residues within 4Å: Chain A: L.58, L.59, Q.72 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.72 Water bridges: A:Q.72

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

CL.8: 6 residues within 4Å: Chain A: I.17, Q.18, P.19, D.47, S.48 Ligands: NA.6 Ligand excluded by PLIP

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

2018-10-24

Peptides

Ribonuclease K6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease K6

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