SMTL ID : 6dcc.2 (1 other biounit)

Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

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

SAH.1: 21 residues within 4Å: Chain A: Y.35, G.36, N.37, Y.41, Y.42, R.53, L.70, G.71, N.73, D.94, I.95, L.99, G.178, N.179, Y.180, V.181, L.201, S.202, L.203, W.211 Chain B: X.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.41, A:N.73 Hydrogen bonds: A:Y.42, A:G.71, A:G.71, A:N.73, A:N.73, A:I.95, A:N.179, A:Y.180, A:L.201 Water bridges: A:L.201 Salt bridges: A:R.45, A:R.53 SAH.3: 21 residues within 4Å: Chain C: Y.35, G.36, N.37, Y.41, Y.42, R.53, L.70, G.71, N.73, D.94, I.95, L.99, G.178, N.179, Y.180, V.181, L.201, S.202, L.203, W.211 Chain D: X.1 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.41, C:N.73 Hydrogen bonds: C:Y.42, C:G.71, C:G.71, C:N.73, C:N.73, C:I.95, C:N.179, C:Y.180, C:L.201 Water bridges: C:L.201 Salt bridges: C:R.45, C:R.53 SAH.5: 21 residues within 4Å: Chain E: Y.35, G.36, N.37, Y.41, Y.42, R.53, L.70, G.71, N.73, D.94, I.95, L.99, G.178, N.179, Y.180, V.181, L.201, S.202, L.203, W.211 Chain F: X.1 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:Y.41, E:N.73 Hydrogen bonds: E:Y.42, E:G.71, E:G.71, E:N.73, E:N.73, E:I.95, E:N.179, E:Y.180, E:L.201 Water bridges: E:L.201 Salt bridges: E:R.45, E:R.53

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

SO4.2: 5 residues within 4Å: Chain A: I.100, R.104, V.176, T.177 Chain E: R.259 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain A Salt bridges: E:R.259, A:R.104 Hydrogen bonds: A:T.177, A:T.177 SO4.4: 5 residues within 4Å: Chain A: R.259 Chain C: I.100, R.104, V.176, T.177 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Salt bridges: A:R.259, C:R.104 Hydrogen bonds: C:T.177, C:T.177 SO4.6: 5 residues within 4Å: Chain C: R.259 Chain E: I.100, R.104, V.176, T.177 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:T.177, E:T.177 Salt bridges: E:R.104, C:R.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE. Nat. Chem. Biol. (2019)

Release Date

2018-12-19

Peptides

7SK snRNA methylphosphate capping enzyme: ACE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

7SK snRNA methylphosphate capping enzyme

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