SMTL ID : 2igt.1 (1 other biounit)

Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: F.134, F.161, Y.163, D.182, A.183, S.184, A.187, E.210, D.211, A.212, D.232, P.233, P.234, G.237, R.238, G.239, W.245, Y.274 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.134 Hydrogen bonds: A:Y.163, A:A.183, A:S.184, A:D.211, A:A.212, A:D.232, A:R.238 Water bridges: A:Y.274, C:R.100, C:R.100 SAM.7: 17 residues within 4Å: Chain B: F.134, F.161, Y.163, D.182, A.183, S.184, A.187, E.210, D.211, A.212, D.232, P.234, G.237, R.238, G.239, W.245, Y.274 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.134 Hydrogen bonds: B:Y.163, B:A.183, B:S.184, B:D.211, B:D.211, B:A.212, B:D.232, B:R.238 Water bridges: B:D.232, B:Y.274, A:R.100, A:R.100 SAM.11: 17 residues within 4Å: Chain C: F.134, F.161, Y.163, D.182, A.183, S.184, A.187, E.210, D.211, A.212, D.232, P.234, G.237, R.238, G.239, W.245, Y.274 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.134 Hydrogen bonds: C:Y.163, C:A.183, C:S.184, C:D.211, C:A.212, C:D.232, C:R.238 Water bridges: C:Y.274, B:R.100, B:R.100

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.210, F.215, R.218, R.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.210, A:R.218, A:R.222, A:R.222 GOL.12: 7 residues within 4Å: Chain B: R.102, F.103, P.104 Chain C: M.22, Q.217, E.220, I.257 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.102, B:R.102, B:P.104, C:Q.217

6 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: S.184, K.185, K.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.185, A:K.186 Water bridges: A:S.184 Salt bridges: A:K.186 ACY.4: 4 residues within 4Å: Chain A: K.185, I.188, G.189, K.192 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.185 Hydrogen bonds: A:K.185 Salt bridges: A:K.185, A:K.192 ACY.5: 2 residues within 4Å: Chain A: L.37, R.326 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.37 Water bridges: A:W.143 Salt bridges: A:R.326 ACY.13: 3 residues within 4Å: Chain C: S.263, P.264, A.294 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.259 ACY.14: 4 residues within 4Å: Chain C: R.63, V.81, N.84, L.310 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.81, C:L.310 Hydrogen bonds: C:N.84 Water bridges: C:R.63, C:R.63 Salt bridges: C:R.63 ACY.15: 4 residues within 4Å: Chain C: E.210, F.215, R.218, R.222 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.218, C:R.222

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 7 residues within 4Å: Chain A: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.66, A:V.131, A:G.132, A:V.133, A:Y.163 Water bridges: A:R.66, A:R.66, A:V.133 FMT.8: 3 residues within 4Å: Chain A: R.100 Chain B: M.213, K.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.100 FMT.9: 7 residues within 4Å: Chain B: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.66, B:R.66, B:V.131, B:G.132, B:V.133, B:Y.163 Water bridges: B:V.133 FMT.10: 3 residues within 4Å: Chain B: S.184, K.185, K.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.185, B:K.186 Water bridges: B:K.186 FMT.16: 7 residues within 4Å: Chain C: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.66, C:R.66, C:V.131, C:G.132, C:V.133 Water bridges: C:V.133 FMT.17: 3 residues within 4Å: Chain C: S.184, K.185, K.186 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.185, C:K.186 Water bridges: C:S.184 FMT.18: 3 residues within 4Å: Chain B: R.100 Chain C: M.213, K.214 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.100 Water bridges: C:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the SAM Dependent Methyltransferase from Agrobacterium tumefaciens. To be Published

Release Date

2006-10-24

Peptides

SAM dependent methyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SAM dependent methyltransferase

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