SMTL ID : 6uk5.1

Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: D.110, L.111, G.112, V.113, T.114, A.143, H.144 No protein-ligand interaction detected (PLIP) PEG.5: 6 residues within 4Å: Chain B: D.110, L.111, G.112, V.113, A.143, H.144 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.112

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

SAM.2: 25 residues within 4Å: Chain A: F.18, Y.26, W.37, D.60, G.62, C.63, G.64, T.65, A.67, H.68, L.82, E.83, L.84, A.85, M.88, G.104, D.105, M.106, R.107, L.121, F.122, A.124, F.127, L.128 Ligands: 1PE.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:W.37, A:G.62, A:C.63, A:H.68, A:E.83, A:L.84, A:A.85, A:D.105, A:M.106, A:R.107, A:R.107 Salt bridges: A:H.68 SAM.6: 23 residues within 4Å: Chain B: Y.26, W.37, D.60, G.62, C.63, G.64, T.65, H.68, L.82, E.83, L.84, A.85, M.88, G.104, D.105, M.106, R.107, L.121, F.122, A.124, F.127, L.128 Ligands: 1PE.8 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.122 Hydrogen bonds: B:Y.26, B:W.37, B:H.68, B:E.83, B:L.84, B:A.85, B:D.105, B:M.106, B:L.121 Salt bridges: B:H.68

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

ACT.3: 6 residues within 4Å: Chain A: Y.30, K.35, F.122, T.242, R.244 Ligands: 1PE.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.30, A:K.35 Salt bridges: A:K.35, A:R.244 ACT.7: 5 residues within 4Å: Chain B: Y.30, K.35, F.122, T.242, R.244 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.35 Salt bridges: B:K.35, B:R.244

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 19 residues within 4Å: Chain A: M.17, F.18, H.22, Y.26, Y.30, F.122, T.123, F.127, W.156, P.159, F.162, Y.166, S.185, T.192, M.194, E.196, L.215 Ligands: SAM.2, ACT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.30 Water bridges: A:H.22, A:Y.30 1PE.8: 13 residues within 4Å: Chain B: Y.26, Y.30, M.88, F.122, T.123, F.127, W.156, M.194, Q.211, G.213, L.214, L.215 Ligands: SAM.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.123, B:L.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alvarado, S.K. et al., Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis. To Be Published

Release Date

2020-10-07

Peptides

CalS10: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CalS10