SMTL ID : 4blw.1 (1 other biounit)

Crystal structure of Escherichia coli 23S rRNA (A2030-N6)- methyltransferase RlmJ in complex with S-adenosylhomocysteine (AdoHcy) and Adenosine monophosphate (AMP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 10 residues within 4Å: Chain A: Y.4, H.9, N.12, E.60, W.195, V.199, R.233, G.234, M.235 Ligands: NA.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.4, A:Y.4, A:N.12, A:M.235 pi-Stacking: A:H.9, A:H.9

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 21 residues within 4Å: Chain A: L.2, Y.4, H.6, K.18, H.19, D.40, T.41, H.42, A.43, G.44, G.99, S.100, E.118, L.119, H.120, D.123, A.142, D.143, G.144, D.164, P.166 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:H.42, A:G.44, A:S.100, A:S.100, A:L.119, A:D.143, A:G.144, A:D.164, A:D.164 Water bridges: A:Y.4, A:R.5 Salt bridges: A:H.6, A:K.18, A:H.19 pi-Cation interactions: A:H.42

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.185, R.186, F.187, A.188 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.186, A:A.188 Water bridges: A:T.189 GOL.4: 3 residues within 4Å: Chain A: V.155, S.156, R.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156, A:R.157

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

EDO.5: 3 residues within 4Å: Chain A: Y.184, A.188 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: H.13, E.60, E.63 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.63, A:R.67, A:R.67, A:L.264, A:L.264 EDO.7: 3 residues within 4Å: Chain A: N.83, H.87, L.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83, A:L.106 EDO.8: 10 residues within 4Å: Chain A: S.7, F.8, H.9, A.10, L.50, A.55, T.58, G.59, E.60, Y.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.7, A:A.55, A:E.60, A:Y.61 EDO.9: 3 residues within 4Å: Chain A: P.228, T.269, G.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.270 EDO.10: 2 residues within 4Å: Chain A: P.266, A.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.266 EDO.11: 5 residues within 4Å: Chain A: K.30, L.106, L.107, L.108, R.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.106 Water bridges: A:K.30, A:K.30 EDO.12: 8 residues within 4Å: Chain A: L.39, Q.115, L.116, T.117, R.138, E.140, Q.147, K.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.116, A:R.138, A:E.140, A:K.151 EDO.13: 4 residues within 4Å: Chain A: R.47, R.105, E.130 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.47 Water bridges: A:R.105

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 5 residues within 4Å: Chain A: Y.4, P.165, P.166, W.195 Ligands: AMP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.4

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 3 residues within 4Å: Chain A: H.87, F.88 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.47, A:R.105, A:R.105 Salt bridges: A:H.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punekar, A.S. et al., Structural and Functional Insights Into the Molecular Mechanism of Rrna M6A Methyltransferase Rlmj. Nucleic Acids Res. (2013)

Release Date

2013-08-21

Peptides

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J

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