SMTL ID : 5et4.1

Structure of RNase A-K7H/R10H in complex with 3'-CMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 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, D.121, A.122 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.43 Hydrogen bonds: A:Q.11, A:H.12, A:K.41, A:T.45, A:T.45, A:T.45, A:F.120 Water bridges: A:K.66, A:H.119, A:S.123 Salt bridges: A:H.12, A:K.41, A:H.119 C3P.2: 10 residues within 4Å: Chain B: Q.11, H.12, K.41, V.43, N.44, T.45, H.119, F.120, D.121, A.122 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.43 Hydrogen bonds: B:Q.11, B:H.12, B:K.41, B:T.45, B:T.45, B:T.45, B:F.120 Water bridges: B:D.83, B:D.83, B:S.123 Salt bridges: B:H.12, B:K.41, B:H.119 C3P.3: 12 residues within 4Å: Chain C: H.7, Q.11, H.12, K.41, V.43, N.44, T.45, H.119, F.120, D.121, A.122, S.123 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.43 Hydrogen bonds: C:H.7, C:Q.11, C:H.12, C:K.41, C:T.45, C:T.45, C:T.45, C:F.120, C:S.123 Water bridges: C:H.12, C:V.118 Salt bridges: C:H.12, C:K.41, C:H.119 C3P.5: 10 residues within 4Å: Chain D: H.7, Q.11, H.12, K.41, V.43, N.44, T.45, H.119, F.120, A.122 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:H.7, D:Q.11, D:H.12, D:K.41, D:T.45, D:T.45, D:T.45, D:F.120, D:S.123 Water bridges: D:K.66, D:V.118 Salt bridges: D:H.12, D:K.41, D:H.119

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 3 residues within 4Å: Chain C: T.99, T.100, Q.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.99, C:Q.101

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

2016-11-30

Peptides

Ribonuclease pancreatic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Ribonuclease pancreatic