SMTL ID : 6zxw.1

Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex bound to sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 17 residues within 4Å: Chain A: P.183, M.184, G.186, D.205, F.206, I.207, I.210, G.230, D.231, A.232, D.248, Y.249, P.250, Y.251, R.253, L.264 Ligands: EDO.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.186, A:F.206, A:D.231, A:A.232, A:D.248, A:D.248, A:Y.251 Water bridges: A:T.187, A:D.248, A:Y.251 Salt bridges: A:R.253 pi-Stacking: A:F.206, A:F.206

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

EDO.2: 4 residues within 4Å: Chain A: F.206, K.233, L.264 Ligands: SFG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.233, A:K.233 EDO.3: 7 residues within 4Å: Chain A: L.252, A.258, G.259, T.260, L.261, D.262, I.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.259, A:L.261, A:D.262 EDO.4: 5 residues within 4Å: Chain A: I.160, K.161, L.164, E.305, R.313 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.159, A:K.161, A:R.313, A:R.313 Water bridges: A:K.161 EDO.5: 5 residues within 4Å: Chain A: E.219, I.223, E.224, G.225 Chain B: K.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.224, A:G.225 EDO.6: 5 residues within 4Å: Chain A: E.219, Y.220, Y.221, G.222 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.219 EDO.7: 6 residues within 4Å: Chain A: R.139, D.140, Q.143, F.144, R.147, R.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.147, A:R.147, A:R.166, A:R.166 EDO.10: 5 residues within 4Å: Chain A: M.1, F.3, Y.43, A.44, G.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.45 EDO.11: 3 residues within 4Å: Chain A: Y.220, Y.221 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.220 EDO.12: 3 residues within 4Å: Chain A: Y.32, Q.33, F.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.32, A:F.34, A:F.34 EDO.13: 4 residues within 4Å: Chain A: K.92, G.93, A.96, L.97 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.97

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 4 residues within 4Å: Chain A: R.139, T.141, F.144, K.163 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.139, A:K.163 ACY.9: 7 residues within 4Å: Chain A: G.195, G.198, I.199, N.200, P.201, I.223, E.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.200, A:E.224

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

SO4.14: 3 residues within 4Å: Chain A: Y.80, D.81, R.82 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.81, A:D.81, A:R.82 Salt bridges: A:R.82 SO4.15: 4 residues within 4Å: Chain A: K.92, G.93, K.94, T.95 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.93, A:K.94, A:T.95 Water bridges: A:A.96 Salt bridges: A:K.92, A:K.94

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 4 residues within 4Å: Chain B: C.11, C.14, C.37, C.40 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.11, B:C.14, B:C.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Functional and structural characterization of the Trm11-Trm112 m2G10 tRNA methyltransferase complex. Nucleic Acids Res. (2020)

Release Date

2020-09-23

Peptides

tRNA (Guanine(10)-N2)-dimethyltransferase: A
Uncharacterized protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

tRNA (Guanine(10)-N2)-dimethyltransferase

Uncharacterized protein