SMTL ID : 5yf1.1

Crystal structure of CARNMT1 bound to carnosine and SFG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 21 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 Ligands: 8V0.2, ACT.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.270 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:F.266, A:Y.277 Water bridges: A:D.121, A:C.265, A:Y.339 Salt bridges: A:R.120 pi-Stacking: A:F.267, A:F.267 SFG.5: 20 residues within 4Å: Chain B: 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 Ligands: 8V0.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.270 Hydrogen bonds: 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:F.266, 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 8V0: (2~{S})-2-(3-azanylpropanoylamino)-3-(1~{H}-imidazol-4-yl)propanoic acid(Non-covalent)

8V0.2: 9 residues within 4Å: Chain A: F.266, D.269, P.296, L.298, H.300, Y.339, Y.349, Y.351 Ligands: SFG.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.339, A:Y.351 Hydrogen bonds: A:D.269, A:Y.351 Water bridges: A:S.113, A:Y.339, A:T.340, A:Y.349, A:Y.349, A:Y.349 Salt bridges: A:H.300 pi-Stacking: A:F.266, A:H.300 8V0.6: 10 residues within 4Å: Chain B: F.266, D.269, P.296, L.298, H.300, Y.339, T.340, Y.349, Y.351 Ligands: SFG.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.339 Hydrogen bonds: B:D.269, B:T.340, B:Y.351, B:Y.351 Water bridges: B:Y.339, B:Y.349, B:Y.349, B:Y.349, B:Y.351 Salt bridges: B:H.300 pi-Stacking: B:F.266, B:H.300

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

ACT.3: 6 residues within 4Å: Chain A: K.110, T.114, S.184, F.186, M.187 Ligands: SFG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.184 Salt bridges: A:K.110 ACT.9: 6 residues within 4Å: Chain B: L.142, F.145, K.147, P.152, L.174, Y.176 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.142

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

EDO.4: 4 residues within 4Å: Chain A: Q.57, F.58, S.219 Chain B: D.316 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.219, A:S.219 Water bridges: A:L.55 EDO.10: 5 residues within 4Å: Chain A: R.218 Chain B: Y.314, E.315, K.318, E.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.318, B:E.331, B:E.333 EDO.11: 4 residues within 4Å: Chain A: D.316 Chain B: Q.57, F.58, S.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.219

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 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.8: 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

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