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SMTL ID : 8c3b.1

X-ray structure of RNase A upon reaction with a Ruthenium(II)-arene Complexed with Glycosylated Carbene Ligands (5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-dimer

Ligands

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

SO4.1:

6 residues within 4Å:

Chain A: Q.11, H.12, K.41, V.118, H.119, F.120

11 PLIP interactions:

11 interactions with chain A

Hydrogen bonds: A:Q.11, A:Q.11, A:F.120, A:F.120
Water bridges: A:K.41, A:K.41, A:H.119, A:H.119
Salt bridges: A:H.12, A:K.41, A:H.119

1 x R6U: (1,3-dimethylimidazol-1-ium-2-yl)-tris(oxidanyl)ruthenium(Non-covalent)

R6U.2:

3 residues within 4Å:

Chain A: T.78, H.105, V.124

1 PLIP interactions:

1 interactions with chain A

Metal complexes: A:H.105

1 x T9L: (1,3-dimethylimidazol-1-ium-2-yl)-tetrakis(oxidanyl)ruthenium(Non-covalent)

T9L.3:

4 residues within 4Å:

Chain B: K.66, H.119, F.120, D.121

5 PLIP interactions:

5 interactions with chain B

Water bridges: B:Q.11, B:Q.11, B:K.41, B:K.41
Metal complexes: B:H.119

1 x T9U: (1,3-dimethyl-2~{H}-imidazol-2-yl)-oxidanyl-oxidanylidene-ruthenium(Non-covalent)

T9U.4:

4 residues within 4Å:

Chain B: Q.74, T.78, H.105, V.124

1 PLIP interactions:

1 interactions with chain B

Metal complexes: B:H.105

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Annunziata, A. et al., Ruthenium(II)–Arene Complexes with Glycosylated NHC-Carbene Co-Ligands: Synthesis, Hydrolytic Behavior, and Binding to Biological Molecules. Organometallics (2023)

Release Date

2024-01-10

Peptides

Ribonuclease pancreatic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Ribonuclease pancreatic

Toggle Identical (AB)

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1a2w.1 | 1afk.1 | 1afk.2 | 1afl.1 | 1afl.2 | 1afu.1 | 1afu.2 | 1aqp.1 | 1bel.1 | 1bzq.1 | 1bzq.2 | 1bzq.3 | 1bzq.4 | 1dfj.1 | 1eos.1 | 1eos.2 | 1eow.1 | 1f0v.1 | 1f0v.2 | 1f0v.3 | 1f0v.4 | 1fs3.1 | 1jn4.1 | 1jn4.2 | 1js0.1 | 1jvt.1 | 1jvt.2 | 1jvu.1 | 1jvu.2 | 1jvv.1 more...less...

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