SMTL ID : 7phd.1

Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-decarboxylase TamK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.125, R.159 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.148, A:Y.148 Salt bridges: A:R.125, A:R.159 SO4.2: 6 residues within 4Å: Chain A: P.251, L.252, R.254, K.255, E.282, A.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.252, A:L.252 Water bridges: A:K.255 Salt bridges: A:K.255 SO4.3: 3 residues within 4Å: Chain A: P.269, D.270, H.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.271 Water bridges: A:H.271, A:H.271 Salt bridges: A:H.271 SO4.7: 2 residues within 4Å: Chain B: R.125, R.159 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.159, B:R.159 Salt bridges: B:R.125, B:R.159

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: R.138, T.139 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain B: T.303, T.305, S.306, P.351, Y.355 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.305 GOL.9: 3 residues within 4Å: Chain B: R.295, G.302, D.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.295, B:R.295, B:S.300, B:D.356

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

SAM.5: 19 residues within 4Å: Chain A: Y.153, R.163, F.166, L.170, F.178, G.197, G.198, G.199, E.220, M.221, G.246, D.247, F.248, F.249, S.262, F.263, N.267, W.268 Ligands: 3VL.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.163, A:R.163, A:G.197, A:D.247, A:D.247, A:F.248 Water bridges: A:L.170, A:S.262, A:S.262, A:S.262 pi-Stacking: A:Y.153, A:F.248, A:F.248 SAM.10: 19 residues within 4Å: Chain B: Y.153, R.163, F.166, L.170, F.178, G.197, G.198, G.199, E.220, M.221, G.246, D.247, F.248, F.249, S.262, F.263, N.267, W.268 Ligands: 3VL.11 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.163, B:R.163, B:G.197, B:D.247, B:D.247, B:F.248, B:S.262 Water bridges: B:Y.153, B:S.262, B:S.262, B:S.262, B:N.267 pi-Stacking: B:Y.153, B:F.248

2 x 3VL: methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate(Non-covalent)

3VL.6: 16 residues within 4Å: Chain A: W.116, V.123, F.152, F.166, L.170, D.173, A.177, F.178, F.263, N.267, V.312, L.313, R.316, M.317, F.320 Ligands: SAM.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.116, A:F.152, A:F.166, A:F.166, A:L.313, A:F.320 Hydrogen bonds: A:D.173, A:N.267, A:N.267, A:R.316 Salt bridges: A:R.316 3VL.11: 20 residues within 4Å: Chain B: W.116, F.152, Y.153, F.166, L.170, D.173, A.177, F.178, F.263, N.267, H.293, Y.309, L.313, R.316, M.317, F.320, L.321, P.354, L.357 Ligands: SAM.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.116, B:F.152, B:L.170, B:F.263, B:Y.309, B:L.313, B:F.320, B:L.321, B:P.354, B:L.357 Hydrogen bonds: B:Y.153, B:Y.153, B:N.267, B:Y.309, B:R.316 pi-Stacking: B:F.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dinis, P. et al., Evolution-inspired engineering of anthracycline methyltransferases. Pnas Nexus (2023)

Release Date

2022-09-07

Peptides

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein