SMTL ID : 8h1b.1

Crystal structure of MnmM from S. aureus complexed with SAM and tRNA anti-codon stem loop (ASL) (1.55 A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 23 residues within 4Å: Chain A: A.27, T.28, C.29, G.30, N.31, G.32, N.33, D.34, D.51, I.52, Q.53, G.76, H.77, E.78, N.98, L.99, G.100, Y.101, L.102, P.103, V.110, T.111 Chain C: U.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.98 Hydrogen bonds: A:T.28, A:G.30, A:N.31, A:N.31, A:G.32, A:N.33, A:N.33, A:D.34, A:Q.53, A:H.77, A:E.78 Water bridges: A:D.34, A:T.115 pi-Stacking: A:H.77 SAM.2: 23 residues within 4Å: Chain B: A.27, T.28, C.29, G.30, N.31, G.32, N.33, D.34, D.51, I.52, Q.53, G.76, H.77, E.78, N.98, L.99, G.100, Y.101, L.102, P.103, V.110, T.111 Chain D: U.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:T.28, B:G.30, B:N.31, B:N.31, B:G.32, B:N.33, B:N.33, B:D.34, B:Q.53, B:H.77, B:E.78, B:T.115 Water bridges: B:T.28, B:T.28, B:C.29 pi-Stacking: B:H.77

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

NA.3: 2 residues within 4Å: Chain C: U.9, G.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, G. et al., Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Nucleic Acids Res. (2023)

Release Date

2023-01-25

Peptides

rRNA methylase YtqB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

rRNA methylase YtqB

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