SMTL ID : 2q66.1

Structure of Yeast Poly(A) Polymerase with ATP and oligo(A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x A- A- A- A- A: 5'-R(P*AP*AP*AP*AP*A)-3'(Non-covalent)

A-A-A-A-A.1: 31 residues within 4Å: Chain A: Y.83, D.96, D.98, V.132, D.134, A.135, F.136, V.137, I.139, K.141, A.150, I.152, R.182, N.222, I.223, Q.290, M.306, C.307, H.310, N.311, G.376, L.377, S.380, K.381, R.383, L.384, K.388, L.487 Ligands: EDO.2, EDO.3, ATP.5 Protein-ligand interaction information (PLIP) not available

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 1 residues within 4Å: Ligands: A-A-A-A-A.1 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: D.134, A.135, F.136 Ligands: A-A-A-A-A.1 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: Y.243, R.254, I.257, I.258 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.12, G.13, A.246, V.250, R.254 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: K.30, F.35 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: N.19, N.22, D.23, C.247 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: L.21, S.24, S.340, W.341 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: I.5, P.272, I.273 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: E.128, A.130, K.141, I.142, K.143 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.56, Y.60, R.74, G.77 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: K.347, F.351, F.401, K.403, F.405, V.517 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: R.217, K.347, D.349 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: E.28, E.32, R.216, A.342, F.345, E.346 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: E.447, D.451 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: V.45, L.48, K.49 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: F.356, F.466, K.474, V.475 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: L.163, S.164 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.96, D.98 Ligands: ATP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:D.98, H2O.16

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 16 residues within 4Å: Chain A: Y.83, G.84, S.85, S.95, D.96, D.98, G.186, K.211, Y.220, N.222, G.229, V.230, M.306, A.308 Ligands: A-A-A-A-A.1, MG.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.85, A:S.85, A:S.95, A:N.222, A:N.222 Water bridges: A:G.84, A:G.84, A:Y.86, A:Y.86, A:D.96, A:D.96, A:D.96, A:T.190, A:K.211, A:K.211, A:Q.215, A:G.229, A:G.229, A:V.230, A:V.230 Salt bridges: A:K.211, A:K.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balbo, P.B. et al., Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis. Structure (2007)

Release Date

2007-08-28

Peptides

Poly(A) polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly(A) polymerase