SMTL ID : 2yx1.3 (2 other biounits)

Crystal structure of M.jannaschii tRNA m1G37 methyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

10 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 2 residues within 4Å: Chain A: H.227, E.230 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.227, A:E.230, H2O.5 ZN.2: 1 residues within 4Å: Chain A: H.243 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.243, H2O.1, H2O.5 ZN.3: 5 residues within 4Å: Chain A: F.303, E.304, C.307, D.308, C.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:F.303, A:C.307, A:C.307, A:C.309 ZN.4: 2 residues within 4Å: Chain A: Y.177 Ligands: SFG.5 No protein-ligand interaction detected (PLIP) ZN.6: 2 residues within 4Å: Chain B: H.11, I.56 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.11 ZN.7: 3 residues within 4Å: Chain B: K.175, H.227, E.230 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.227, B:E.230 ZN.8: 5 residues within 4Å: Chain B: F.303, E.304, C.307, D.308, C.309 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:F.303, B:C.307, B:C.307, B:C.309 ZN.9: 1 residues within 4Å: Ligands: SFG.12 No protein-ligand interaction detected (PLIP) ZN.10: 3 residues within 4Å: Chain A: D.113 Chain B: H.271, K.272 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.113, A:D.113, B:H.271 ZN.11: 1 residues within 4Å: Chain B: K.318 No protein-ligand interaction detected (PLIP)

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.5: 19 residues within 4Å: Chain A: Y.177, F.178, R.186, M.202, F.203, A.204, G.205, P.208, F.209, D.223, I.224, N.225, S.250, D.251, V.252, N.265, L.266, F.273 Ligands: ZN.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.203, A:L.266 Hydrogen bonds: A:Y.177, A:F.203, A:G.205, A:I.224, A:D.251, A:D.251, A:V.252, A:N.265 Water bridges: A:S.179, A:F.209, A:N.225, A:N.265, A:N.265 Salt bridges: A:R.186 pi-Stacking: A:F.203, A:F.203 SFG.12: 18 residues within 4Å: Chain B: F.178, R.186, M.202, F.203, A.204, G.205, P.208, F.209, D.223, I.224, N.225, S.250, D.251, V.252, N.265, L.266, F.273 Ligands: ZN.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.203, B:L.266 Hydrogen bonds: B:F.203, B:G.205, B:I.224, B:D.251, B:V.252, B:N.265 Water bridges: B:Y.177, B:F.209, B:N.225, B:N.225, B:N.225, B:N.225, B:N.265 Salt bridges: B:R.186 pi-Stacking: B:F.203, B:F.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto-Ito, S. et al., Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins (2008)

Release Date

2008-04-22

Peptides

Hypothetical protein MJ0883: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical protein MJ0883

Related Entries With Identical Sequence