SMTL ID : 2xzp.1

Upf1 helicase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-trimer

Ligands

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: R.131, P.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.131, A:R.131 GOL.2: 10 residues within 4Å: Chain A: L.218, G.222, N.223, G.224, P.225, V.226, F.339, R.340, S.341 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.218, A:P.225, A:R.340, A:S.341, A:S.341 Water bridges: A:V.226 GOL.3: 4 residues within 4Å: Chain A: N.223, G.224, R.340 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.223, A:N.223, A:G.224 GOL.6: 2 residues within 4Å: Chain B: R.131, P.332 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.131, B:R.131 GOL.7: 10 residues within 4Å: Chain B: L.218, G.222, N.223, G.224, P.225, V.226, F.339, R.340, S.341 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.218, B:P.225, B:R.340, B:S.341, B:S.341 Water bridges: B:V.226 GOL.8: 4 residues within 4Å: Chain B: N.223, G.224, R.340 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.223, B:N.223, B:G.224 GOL.11: 2 residues within 4Å: Chain C: R.131, P.332 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.131, C:R.131 GOL.12: 10 residues within 4Å: Chain C: L.218, G.222, N.223, G.224, P.225, V.226, F.339, R.340, S.341 Ligands: GOL.13 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.218, C:P.225, C:R.340, C:S.341, C:S.341 Water bridges: C:V.226 GOL.13: 4 residues within 4Å: Chain C: N.223, G.224, R.340 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.223, C:N.223, C:G.224

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 9 residues within 4Å: Chain A: P.202, P.203, G.204, T.205, K.207, Q.374, R.412, G.540, R.574 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.204, A:Q.374, A:G.540, A:G.540 Salt bridges: A:K.207, A:R.412, A:R.412, A:R.574 MLI.5: 3 residues within 4Å: Chain A: G.204, G.206, V.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.205 Salt bridges: A:K.242, A:R.412 MLI.9: 9 residues within 4Å: Chain B: P.202, P.203, G.204, T.205, K.207, Q.374, R.412, G.540, R.574 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.204, B:Q.374, B:G.540, B:G.540 Salt bridges: B:K.207, B:R.412, B:R.412, B:R.574 MLI.10: 3 residues within 4Å: Chain B: G.204, G.206, V.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.205 Salt bridges: B:K.242, B:R.412 MLI.14: 9 residues within 4Å: Chain C: P.202, P.203, G.204, T.205, K.207, Q.374, R.412, G.540, R.574 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.204, C:Q.374, C:G.540, C:G.540 Salt bridges: C:K.207, C:R.412, C:R.412, C:R.574 MLI.15: 3 residues within 4Å: Chain C: G.204, G.206, V.209 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.205 Salt bridges: C:K.242, C:R.412

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chakrabarti, S. et al., Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2. Mol.Cell (2011)

Release Date

2011-03-30

Peptides

REGULATOR OF NONSENSE TRANSCRIPTS 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

REGULATOR OF NONSENSE TRANSCRIPTS 1

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