SMTL ID : 4fak.1

Crystal Structure of OrfX in Complex with S-Adenosylmethionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 18 residues within 4Å: Chain A: L.80, E.81, I.82, I.111, G.112, G.113, S.114, G.116, L.129, S.130, F.131, S.132, M.134, T.135, F.136, M.141 Chain B: K.163 Ligands: PO4.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.80, A:G.112, A:G.113, A:F.131, A:S.132, A:M.134, A:F.136, B:K.163 Water bridges: A:L.117, A:L.117, A:L.117, A:L.117 SAM.4: 18 residues within 4Å: Chain A: K.163 Chain B: L.80, E.81, I.82, I.111, G.112, G.113, S.114, G.116, L.129, S.130, F.131, S.132, M.134, T.135, F.136, M.141 Ligands: PO4.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.80, B:G.112, B:G.113, B:F.131, B:S.132, B:M.134, B:F.136, A:K.163 Water bridges: B:L.117, B:L.117, B:L.117, B:L.117

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 7 residues within 4Å: Chain A: P.73, S.75, T.76, Q.104, Q.123, R.124, N.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.124, A:R.124, A:S.125, A:N.126 Water bridges: A:Q.123, A:Q.123 PG4.5: 7 residues within 4Å: Chain B: P.73, S.75, T.76, Q.104, Q.123, R.124, N.126 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.124, B:R.124, B:S.125, B:N.126 Water bridges: B:Q.123, B:Q.123

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: S.114, P.137, H.138 Chain B: R.151, K.163 Ligands: SAM.1 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:H.138, B:R.151 Water bridges: A:Q.139, B:R.151, B:R.151, B:Y.161, B:K.163, B:K.163 Salt bridges: A:H.138, B:K.163 PO4.6: 6 residues within 4Å: Chain A: R.151, K.163 Chain B: S.114, P.137, H.138 Ligands: SAM.4 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.151, B:H.138 Water bridges: A:R.151, A:R.151, A:Y.161, A:K.163, A:K.163, B:Q.139 Salt bridges: A:K.163, B:H.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boundy, S. et al., Characterization of the Staphylococcus aureus rRNA Methyltransferase Encoded by orfX, the Gene Containing the Staphylococcal Chromosome Cassette mec (SCCmec) Insertion Site. J.Biol.Chem. (2013)

Release Date

2012-06-06

Peptides

Ribosomal RNA large subunit methyltransferase H: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Ribosomal RNA large subunit methyltransferase H