SMTL ID : 5yf0.1

Crystal structure of CARNMT1 bound to SAM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: D.316 Chain B: Q.57, F.58, H.61, S.219 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.219 Water bridges: B:F.58, A:N.319 EDO.2: 4 residues within 4Å: Chain A: Q.250, D.276, D.279, T.280 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.276, A:T.280, B:Q.51 EDO.3: 5 residues within 4Å: Chain A: F.44, Q.52, L.55, P.56, L.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.52 Water bridges: A:Q.52, A:P.56 EDO.6: 5 residues within 4Å: Chain A: Q.57, F.58, H.61, S.219 Chain B: D.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.219 Water bridges: A:F.58

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: T.340, V.341, N.342, M.347, K.348, Y.349 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.341, A:N.342 Hydrogen bonds: A:Y.349 ACT.7: 5 residues within 4Å: Chain B: V.341, N.342, M.347, K.348, Y.349 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.341, B:N.342 Hydrogen bonds: B:Y.349 Water bridges: B:K.116, B:K.116

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

SAM.5: 19 residues within 4Å: Chain A: Q.117, R.120, Y.134, G.161, G.163, N.181, E.182, W.183, S.184, M.187, G.247, D.248, F.249, C.265, F.266, F.267, T.270, Y.277, Y.339 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Q.117, A:Y.134, A:G.161, A:G.161, A:W.183, A:S.184, A:D.248, A:D.248, A:F.249, A:C.265, A:Y.277 Water bridges: A:S.184, A:S.184, A:C.265, A:T.270, A:T.270 Salt bridges: A:R.120 pi-Stacking: A:F.267, A:F.267 SAM.8: 18 residues within 4Å: Chain B: Q.117, R.120, Y.134, G.161, N.181, E.182, W.183, S.184, M.187, G.247, D.248, F.249, C.265, F.266, F.267, T.270, Y.277, Y.339 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.117, B:G.161, B:G.161, B:W.183, B:S.184, B:D.248, B:D.248, B:F.249, B:C.265, B:T.270, B:Y.277 Water bridges: B:C.265 Salt bridges: B:R.120 pi-Stacking: B:F.267, B:F.267

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 2 residues within 4Å: Chain B: S.199, D.232 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.199, B:S.199, B:D.232, H2O.11 CA.10: 1 residues within 4Å: Chain B: D.63 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, R. et al., Molecular basis for histidine N1 position-specific methylation by CARNMT1. Cell Res. (2018)

Release Date

2018-08-01

Peptides

Carnosine N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carnosine N-methyltransferase

Related Entries With Identical Sequence