SMTL ID : 3ggd.1

Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x UNL: UNKNOWN LIGAND

UNL.1: 9 residues within 4Å: Chain A: W.19, L.34, W.35, T.132, H.135, H.136, P.196, F.221 Ligands: SAH.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.132, A:T.132 Salt bridges: A:H.135

1 x CO: COBALT (II) ION(Non-covalent)

CO.2: 3 residues within 4Å: Chain A: D.210, H.244 Ligands: IMD.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.210, A:H.244

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: I.13, N.14, V.15, K.141 Ligand excluded by PLIP

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

SAH.4: 17 residues within 4Å: Chain A: V.15, W.19, W.23, W.35, A.64, C.65, G.66, D.85, V.86, L.108, D.109, G.110, L.111, R.131, T.132, H.136 Ligands: UNL.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:W.23, A:G.66, A:V.86, A:D.109, A:D.109, A:G.110, A:L.111, A:R.131, A:R.131 Water bridges: A:G.68, A:Q.70, A:R.131 Salt bridges: A:R.131 pi-Stacking: A:W.19

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 4 residues within 4Å: Chain A: R.150, D.210, H.244 Ligands: CO.2 No protein-ligand interaction detected (PLIP)

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

SO4.6: 6 residues within 4Å: Chain A: T.166, G.167, C.168, I.169, D.170, I.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.167, A:C.168, A:I.169, A:D.170 SO4.7: 7 residues within 4Å: Chain A: R.80, I.82, S.104, R.106, I.119, E.122, I.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.80 Water bridges: A:R.106, A:R.106 Salt bridges: A:R.106 SO4.8: 3 residues within 4Å: Chain A: K.155, Q.156, K.243 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.243 Salt bridges: A:K.155, A:K.243 SO4.9: 3 residues within 4Å: Chain A: R.49, W.239 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.49

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

EDO.10: 4 residues within 4Å: Chain A: D.36, A.37, N.38, T.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.69, A:T.69 Water bridges: A:N.67 EDO.11: 8 residues within 4Å: Chain A: R.41, A.42, D.46, R.131, I.162, L.220, F.221, Q.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.46, A:R.131, A:Q.222, A:Q.222 EDO.12: 3 residues within 4Å: Chain A: V.44, V.45, P.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.44 EDO.13: 5 residues within 4Å: Chain A: D.125, G.154, K.155, Q.156 Ligands: EDO.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.155, A:Q.156 EDO.14: 2 residues within 4Å: Chain A: E.212, I.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.213, A:I.213 EDO.15: 8 residues within 4Å: Chain A: L.175, Y.179, Q.181, L.182, P.183, H.225, L.227, P.228 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: G.124, D.125, Q.156 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.125 EDO.17: 6 residues within 4Å: Chain A: R.49, G.217, E.218, G.219, W.239 Ligands: SO4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.218 Water bridges: A:R.49 EDO.18: 4 residues within 4Å: Chain A: R.106, L.107, Q.115, Q.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.106, A:L.107

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution. To be published

Release Date

2009-03-31

Peptides

SAM-dependent methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

SAM-dependent methyltransferase