SMTL ID : 5yf2.1

Crystal structure of CARNMT1 bound to anserine and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: R.120, D.121, 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 Ligands: 8V3.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.121, A:Y.134, 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:C.265 Salt bridges: A:R.120 pi-Stacking: A:F.267, A:F.267 SAH.5: 20 residues within 4Å: Chain B: R.120, Y.134, G.161, A.162, 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 Ligands: 8V3.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.161, B:W.183, B:D.248, B:D.248, B:F.249, B:C.265, B:C.265, B:T.270, B:Y.277 Water bridges: B:G.165 Salt bridges: B:R.120 pi-Stacking: B:F.267, B:F.267

2 x 8V3: (2~{S})-2-(3-azanylpropanoylamino)-3-(3-methylimidazol-4-yl)propanoic acid(Non-covalent)

8V3.2: 8 residues within 4Å: Chain A: F.266, D.269, P.296, L.298, Y.339, Y.349, Y.351 Ligands: SAH.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.339 Hydrogen bonds: A:Y.351 Water bridges: A:H.300, A:H.300, A:Y.339 pi-Stacking: A:F.266 8V3.6: 9 residues within 4Å: Chain B: F.266, D.269, P.296, L.298, Y.339, T.340, Y.349, Y.351 Ligands: SAH.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.266, B:Y.339 Hydrogen bonds: B:T.340, B:Y.351, B:Y.351 pi-Stacking: B:F.266 Water bridges: A:Y.349

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.316 Chain B: Q.57, S.219 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: E.41, D.63, R.66 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.63, H2O.6, H2O.8

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 7 residues within 4Å: Chain A: L.336, Y.350, E.352 Chain B: R.217, D.343, L.344, K.348 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.350, B:K.348

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

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