SMTL ID : 3c3p.1 (1 other biounit)

Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: R.42, R.46, W.73 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: A.122, Q.124 Ligand excluded by PLIP

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

EDO.2: 5 residues within 4Å: Chain A: R.53, R.76, A.77, I.78, S.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76 Water bridges: A:Q.56 EDO.3: 4 residues within 4Å: Chain A: Q.58, L.59, R.125, D.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58 Water bridges: A:R.125 EDO.4: 4 residues within 4Å: Chain A: V.6, D.7, S.8, G.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.11 Water bridges: A:G.11, A:D.15 EDO.5: 7 residues within 4Å: Chain A: L.17, L.18, P.19, R.46 Chain B: S.187, T.194, T.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.187 EDO.6: 6 residues within 4Å: Chain A: G.64, D.65, G.66, D.88, N.93, V.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.65, A:D.88 EDO.7: 2 residues within 4Å: Chain A: D.90, D.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.90 EDO.8: 8 residues within 4Å: Chain A: C.134, D.135, N.160, A.161, L.162, R.163, R.164, R.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.134, A:A.161 EDO.9: 6 residues within 4Å: Chain A: F.192, F.193, L.209 Chain B: P.19, R.46 Ligands: PEG.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.192, B:R.46, B:R.46 EDO.14: 6 residues within 4Å: Chain B: V.24, A.27, M.28, I.31, H.96, M.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.96 EDO.15: 6 residues within 4Å: Chain A: R.53, I.54, Q.56 Chain B: K.55, N.153, Y.207 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.56, B:K.55, B:K.55, B:Y.207 Water bridges: A:R.53, A:R.53, A:R.53, B:N.153 EDO.16: 4 residues within 4Å: Chain B: A.140, L.143, E.144, R.189 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.140

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

PEG.10: 6 residues within 4Å: Chain A: Y.49, W.72, W.73, R.76 Chain B: F.193 Ligands: PEG.11 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain A: D.22, R.76 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.76, A:R.76 PEG.12: 4 residues within 4Å: Chain A: L.179, E.181, H.184 Chain B: Y.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.179 PEG.17: 5 residues within 4Å: Chain B: R.53, R.76, A.77, I.78, S.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.78, B:S.79 PEG.18: 7 residues within 4Å: Chain A: P.198 Chain B: I.5, V.6, Q.43, P.198, V.199, G.200 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.5, B:V.6, B:G.200 PEG.19: 7 residues within 4Å: Chain A: F.193, L.209 Chain B: D.22, Y.49, W.73, R.76 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.22, B:D.22, B:R.76 PEG.20: 1 residues within 4Å: Chain B: G.119 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.119 PEG.21: 5 residues within 4Å: Chain B: D.116, P.117, L.118, F.137, R.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.118, B:R.145 Water bridges: B:N.138, B:D.141

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution. To be published

Release Date

2008-02-05

Peptides

Methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase

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