SMTL ID : 2e9z.1

Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP and UTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x C- A- U- G- G- G- C- C- C: 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'(Non-covalent)

C-A-U-G-G-G-C-C-C.1: 35 residues within 4Å: Chain A: R.17, L.108, D.109, E.112, T.115, A.116, R.128, F.162, K.164, V.181, V.183, R.193, H.204, V.215, G.216, C.217, N.218, S.298, G.299, C.300, S.301, A.302, T.303, Y.336, R.416, I.425, R.461 Ligands: G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, UTP.5 Protein-ligand interaction information (PLIP) not available

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

G-G-G-C-C-C-A.2: 28 residues within 4Å: Chain A: D.114, K.164, Y.336, G.337, D.338, D.339, L.386, K.387, R.388, M.403, I.411, R.416, T.419, E.422, K.423, S.426, V.427, L.430 Ligands: C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, C-A-U-G-G-G-C-C-C.1, UTP.5, PPV.6 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.238, D.240, D.339, T.384 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.238, A:D.339 MG.4: 3 residues within 4Å: Chain A: Y.241, D.338 Ligands: UTP.5 No protein-ligand interaction detected (PLIP)

1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.5: 13 residues within 4Å: Chain A: K.164, R.168, R.179, I.180, V.181, S.242, D.245, S.298, D.338 Ligands: C-A-U-G-G-G-C-C-C.1, G-G-G-C-C-C-A.2, MG.4, PPV.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.164 Hydrogen bonds: A:R.168, A:I.180, A:D.245, A:D.245, A:S.298, A:D.338 Water bridges: A:R.179 Salt bridges: A:R.179 pi-Cation interactions: A:R.179

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.6: 6 residues within 4Å: Chain A: E.166, R.179, K.387 Ligands: G-G-G-C-C-C-A.2, G-G-G-C-C-C-A.2, UTP.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.166 Water bridges: A:R.179 Salt bridges: A:R.179, A:R.179, A:K.387, A:K.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrer-Orta, C. et al., Sequential structures provide insights into the fidelity of RNA replication. Proc.Natl.Acad.Sci.Usa (2007)

Release Date

2007-06-26

Peptides

RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent RNA polymerase

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