SMTL ID : 4qpx.1

NV polymerase post-incorporation-like complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

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

U-G-C-C-C-G-G-G.1: 37 residues within 4Å: Chain A: T.116, R.126, N.128, K.166, R.182, L.184, D.242, W.246, D.247, S.300, G.301, T.305, S.306, N.309, Y.341, G.342, D.343, D.344, L.391, R.392, R.393, L.406, S.410, R.413, Q.414, R.419, Q.435, Q.439 Ligands: A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, MN.4, MN.5, GOL.7 Protein-ligand interaction information (PLIP) not available

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

A-C-C-C-G-G-G.2: 38 residues within 4Å: Chain A: S.23, K.25, L.113, T.117, S.118, K.127, A.164, L.165, K.166, D.167, L.184, W.185, G.186, S.187, M.192, K.207, V.217, G.218, M.219, N.220, G.301, V.302, P.303, C.304, Y.341, N.422, S.502, F.503, V.504, N.505 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, GOL.7 Protein-ligand interaction information (PLIP) not available

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: V.211, T.212, L.213, P.214, R.216, R.231, L.337, F.338 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.213, A:R.216, A:R.216, A:R.231, A:F.338 GOL.7: 7 residues within 4Å: Chain A: K.166 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2, A-C-C-C-G-G-G.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.166

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: D.242, D.343, D.344 Ligands: U-G-C-C-C-G-G-G.1, U-G-C-C-C-G-G-G.1, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:D.343, A:D.344, H2O.12 MN.5: 5 residues within 4Å: Chain A: D.242, Y.243, D.343 Ligands: U-G-C-C-C-G-G-G.1, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.242, A:Y.243, A:D.343, H2O.10 MN.6: 3 residues within 4Å: Chain A: D.99, E.205, H.209 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.99, A:E.205, A:H.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zamyatkin, D. et al., Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase. Acta Crystallogr.,Sect.D (2014)

Release Date

2015-04-22

Peptides

Polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyprotein

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