SMTL ID : 6gfk.4 (3 other biounits)

delta-N METTL16 MTase domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

SAH.1: 23 residues within 4Å: Chain A: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.145, P.146, F.148, F.187 Chain C: N.5 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.35 Hydrogen bonds: A:G.70, A:Y.77, A:T.92, A:V.94, A:D.95, A:T.124, A:N.144, A:R.190 Water bridges: A:R.190, A:R.190, C:D.8 Salt bridges: A:R.42 SAH.4: 23 residues within 4Å: Chain B: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.146, F.148, F.187, R.190 Chain F: N.5 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:G.70, B:V.94, B:D.95, B:T.124, B:N.144, B:R.190 Water bridges: B:L.35, B:T.92, F:N.5, F:D.8 Salt bridges: B:R.42 SAH.6: 23 residues within 4Å: Chain A: N.5 Chain C: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.145, P.146, F.148, F.187 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.35 Hydrogen bonds: C:G.70, C:Y.77, C:T.92, C:V.94, C:D.95, C:T.124, C:N.144, C:R.190 Water bridges: C:R.190, C:R.190, A:D.8 Salt bridges: C:R.42 SAH.9: 23 residues within 4Å: Chain D: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.146, F.148, F.187, R.190 Chain E: N.5 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.70, D:V.94, D:D.95, D:T.124, D:N.144, D:R.190 Water bridges: D:L.35, E:N.5, E:D.8 Salt bridges: D:R.42 SAH.11: 23 residues within 4Å: Chain D: N.5 Chain E: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.145, P.146, F.148, F.187 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.70, E:Y.77, E:V.94, E:D.95, E:T.124, E:N.144, E:R.190 Water bridges: E:R.190, D:N.5, D:D.8 Salt bridges: E:R.42 SAH.14: 23 residues within 4Å: Chain B: N.5 Chain F: L.35, P.37, R.42, G.70, T.71, G.72, I.76, Y.77, T.92, E.93, V.94, D.95, C.98, V.120, Q.122, T.124, L.125, N.144, P.145, P.146, F.148, F.187 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.70, F:Y.77, F:V.94, F:D.95, F:T.124, F:N.144, F:R.190 Water bridges: F:T.92, F:R.190, B:N.5, B:D.8 Salt bridges: F:R.42

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

SO4.2: 8 residues within 4Å: Chain A: L.35, L.41, R.42, N.144, M.208, R.242 Chain C: K.7, R.239 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.144, C:R.239 Water bridges: A:R.42 Salt bridges: A:R.42, A:R.242, C:K.7 SO4.3: 1 residues within 4Å: Chain A: R.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:R.13 Salt bridges: A:R.13 Hydrogen bonds: C:E.33 SO4.5: 6 residues within 4Å: Chain B: L.35, R.42, N.144, R.242 Chain F: K.7, R.239 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:N.144 Salt bridges: B:R.42, B:R.242, F:K.7, F:R.239 SO4.7: 8 residues within 4Å: Chain A: K.7, R.239 Chain C: L.35, L.41, R.42, N.144, M.208, R.242 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.144, A:R.239 Water bridges: C:R.42 Salt bridges: C:R.42, C:R.242, A:K.7 SO4.8: 1 residues within 4Å: Chain C: R.13 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.13 Salt bridges: C:R.13 SO4.10: 6 residues within 4Å: Chain D: L.35, R.42, N.144, R.242 Chain E: K.7, R.239 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:N.144 Salt bridges: D:R.42, D:R.242, E:K.7, E:R.239 SO4.12: 7 residues within 4Å: Chain D: K.7, R.239 Chain E: L.35, R.42, N.144, M.208, R.242 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:N.144 Salt bridges: E:R.42, E:R.242, D:K.7, D:R.239 Water bridges: D:K.7 SO4.13: 1 residues within 4Å: Chain E: R.13 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.13 SO4.15: 7 residues within 4Å: Chain B: K.7, R.239 Chain F: L.35, R.42, N.144, M.208, R.242 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain F Water bridges: B:K.7 Salt bridges: B:K.7, B:R.239, F:R.42, F:R.242 Hydrogen bonds: F:N.144 SO4.16: 1 residues within 4Å: Chain F: R.13 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mendel, M. et al., Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development. Mol. Cell (2018)

Release Date

2018-09-19

Peptides

U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

E
B

F
B

U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase

Related Entries With Identical Sequence