SMTL ID : 4oi0.1

bound to ssRNA dinucleotide GC, ADP, AlF4-, and Mg2+(transition state, data set I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x G- C: RNA (5'-R(*GP*C)-3')(Non-covalent)

G-C.1: 13 residues within 4Å: Chain A: T.126, D.154, G.156, Q.157, T.194, S.195, S.197, C.234, G.235, W.236, R.296, R.300 Ligands: ALF.4 Protein-ligand interaction information (PLIP) not available

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: E.19, R.59, A.61, P.125, D.127, V.128, G.129, K.130, T.131, T.132, S.285, G.287, V.288, E.289, R.291 Ligands: MG.3, ALF.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.19, A:D.127, A:V.128, A:G.129, A:K.130, A:T.131, A:T.132, A:T.132, A:S.285, A:E.289 Water bridges: A:R.21, A:T.132, A:R.291, A:R.291 Salt bridges: A:K.130, A:R.291, A:R.291 pi-Stacking: A:F.42, A:F.42

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.131, D.154, N.232 Ligands: ADP.2, ALF.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.131, H2O.1, H2O.1, H2O.1

1 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.4: 12 residues within 4Å: Chain A: P.125, T.126, D.127, K.130, D.154, Q.157, G.235, R.291, R.296 Ligands: G-C.1, ADP.2, MG.3 No protein-ligand interaction detected (PLIP)

2 x SAR: SARCOSINE(Non-covalent)

SAR.5: 1 residues within 4Å: Chain A: Y.80 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.80 SAR.6: 2 residues within 4Å: Chain A: Q.185, Q.217 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.374

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.7: 6 residues within 4Å: Chain A: W.65, L.91, H.94, Y.140, R.143, Q.144 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dikfidan, A. et al., RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1. Mol.Cell (2014)

Release Date

2014-05-14

Peptides

Protein clpf-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein clpf-1

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