SMTL ID : 4m30.1

Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II CLEAVAGE)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 5 residues within 4Å: Chain A: D.44, E.110 Chain D: U.27 Ligands: MG.2, AMP.8 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.44, A:E.110, H2O.1, H2O.3, AMP.8 MG.2: 4 residues within 4Å: Chain A: E.40, E.110 Ligands: MG.1, AMP.8 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.40, A:E.110, H2O.1, H2O.1, AMP.8 MG.3: 5 residues within 4Å: Chain B: D.44, E.110 Chain C: U.27 Ligands: MG.4, AMP.12 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.44, B:E.110, H2O.1, H2O.3, AMP.12 MG.4: 4 residues within 4Å: Chain B: E.40, E.110 Ligands: MG.3, AMP.12 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: B:E.40, B:E.110, H2O.2, AMP.12, AMP.12 MG.6: 3 residues within 4Å: Chain A: D.107 Chain B: E.64 Chain C: A.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain C: A.1, A.2 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain A: E.64 Chain B: D.107 Chain D: A.1 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain D: A.1, A.2 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain D: C.22 No protein-ligand interaction detected (PLIP)

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

MPD.5: 6 residues within 4Å: Chain A: L.20, K.23, I.118 Chain B: V.56, Q.57, K.62 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.62, A:I.118 Hydrogen bonds: A:K.23

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.8: 13 residues within 4Å: Chain A: E.40, F.41, D.44, E.110 Chain B: E.64, S.68, K.71 Chain C: A.1, U.25, A.26 Chain D: U.27 Ligands: MG.1, MG.2 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.40, B:E.64, B:E.64, B:S.68, B:K.71 Water bridges: A:E.40 AMP.12: 13 residues within 4Å: Chain A: E.64, S.68, K.71 Chain B: E.40, F.41, D.44, E.110 Chain C: U.27 Chain D: A.1, U.25, A.26 Ligands: MG.3, MG.4 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.64, A:E.64, A:S.68, A:S.68, A:K.71, B:E.40 Water bridges: B:N.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Court, D.L. et al., RNase III: Genetics and Function; Structure and Mechanism. Annu. Rev. Genet. (2013)

Release Date

2013-12-11

Peptides

Ribonuclease 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribonuclease 3

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