SMTL ID : 5oab.1

A novel crystal form of human RNase6 at atomic resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

monomer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: K.4, R.5 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.4, A:K.4 Salt bridges: A:K.4, A:R.5 PO4.2: 7 residues within 4Å: Chain A: F.12, Q.15, H.16, K.39, H.123, L.124 Ligands: CL.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.15, A:L.124 Water bridges: A:H.16, A:H.16, A:H.123, A:L.124 Salt bridges: A:H.16, A:H.123 PO4.3: 3 residues within 4Å: Chain A: H.37, H.40, K.88 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.40, A:H.40 Salt bridges: A:H.37, A:H.40, A:K.88 PO4.4: 3 residues within 4Å: Chain A: T.85, S.86, R.93 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.25, A:T.85, A:T.85, A:R.93, A:R.93 Salt bridges: A:R.93 PO4.5: 3 residues within 4Å: Chain A: R.67, H.68, N.69 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.68, A:H.68 Water bridges: A:R.67, A:R.67, A:R.67, A:R.67, A:H.68 Salt bridges: A:R.67 PO4.6: 2 residues within 4Å: Chain A: N.25, R.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.25 Water bridges: A:N.25, A:R.93 Salt bridges: A:R.93

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

NA.7: 3 residues within 4Å: Chain A: W.2, K.8 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.8 NA.8: 4 residues within 4Å: Chain A: M.1, W.2, P.3, K.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.2 Water bridges: A:K.4 NA.9: 5 residues within 4Å: Chain A: K.8, W.11, F.12, V.122 Ligands: CL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.12, A:V.122 Water bridges: A:H.123

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

CL.10: 4 residues within 4Å: Chain A: K.8, N.65, H.123 Ligands: NA.7 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain A: W.11, F.12, Q.15, H.16, V.122, H.123 Ligands: PO4.2, NA.9 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: T.7, K.8, A.9, Q.111 Ligands: K.13 Ligand excluded by PLIP

1 x K: POTASSIUM ION(Non-covalent)

K.13: 5 residues within 4Å: Chain A: W.2, T.7, K.8, Q.111 Ligands: CL.12 No protein-ligand interaction detected (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

2018-08-01

Peptides

Ribonuclease K6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ribonuclease K6

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