SMTL ID : 2igt.2 (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-hexamer

Ligands

6 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 SAM.19: 18 residues within 4Å: Chain D: 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 D, 2 interactions with chain F Hydrophobic interactions: D:F.134 Hydrogen bonds: D:Y.163, D:A.183, D:S.184, D:D.211, D:A.212, D:D.232, D:R.238 Water bridges: D:Y.274, F:R.100, F:R.100 SAM.25: 17 residues within 4Å: Chain E: 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: 2 interactions with chain D, 11 interactions with chain E Water bridges: D:R.100, D:R.100, E:D.232, E:Y.274 Hydrophobic interactions: E:F.134 Hydrogen bonds: E:Y.163, E:A.183, E:S.184, E:D.211, E:D.211, E:A.212, E:D.232, E:R.238 SAM.29: 17 residues within 4Å: Chain F: 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 F, 2 interactions with chain E Hydrophobic interactions: F:F.134 Hydrogen bonds: F:Y.163, F:A.183, F:S.184, F:D.211, F:A.212, F:D.232, F:R.238 Water bridges: F:Y.274, E:R.100, E:R.100

4 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: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.217, B:R.102, B:R.102, B:P.104 GOL.20: 4 residues within 4Å: Chain D: E.210, F.215, R.218, R.222 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.210, D:R.218, D:R.222, D:R.222 GOL.30: 7 residues within 4Å: Chain E: R.102, F.103, P.104 Chain F: M.22, Q.217, E.220, I.257 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Q.217, E:R.102, E:R.102, E:P.104

12 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 ACY.21: 3 residues within 4Å: Chain D: S.184, K.185, K.186 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.185, D:K.186 Water bridges: D:S.184 Salt bridges: D:K.186 ACY.22: 4 residues within 4Å: Chain D: K.185, I.188, G.189, K.192 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.185 Hydrogen bonds: D:K.185 Salt bridges: D:K.185, D:K.192 ACY.23: 2 residues within 4Å: Chain D: L.37, R.326 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.37 Water bridges: D:W.143 Salt bridges: D:R.326 ACY.31: 3 residues within 4Å: Chain F: S.263, P.264, A.294 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.259 ACY.32: 4 residues within 4Å: Chain F: R.63, V.81, N.84, L.310 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:V.81, F:L.310 Hydrogen bonds: F:N.84 Water bridges: F:R.63, F:R.63 Salt bridges: F:R.63 ACY.33: 4 residues within 4Å: Chain F: E.210, F.215, R.218, R.222 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.218, F:R.222

14 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 C, 1 interactions with chain B Water bridges: C:K.214 Hydrogen bonds: B:R.100 FMT.24: 7 residues within 4Å: Chain D: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.66, D:V.131, D:G.132, D:V.133, D:Y.163 Water bridges: D:R.66, D:R.66, D:V.133 FMT.26: 3 residues within 4Å: Chain D: R.100 Chain E: M.213, K.214 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.100 FMT.27: 7 residues within 4Å: Chain E: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.66, E:R.66, E:V.131, E:G.132, E:V.133, E:Y.163 Water bridges: E:V.133 FMT.28: 3 residues within 4Å: Chain E: S.184, K.185, K.186 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.185, E:K.186 Water bridges: E:K.186 FMT.34: 7 residues within 4Å: Chain F: R.66, H.130, V.131, G.132, V.133, F.134, Y.163 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.66, F:R.66, F:V.131, F:G.132, F:V.133 Water bridges: F:V.133 FMT.35: 3 residues within 4Å: Chain F: S.184, K.185, K.186 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.185, F:K.186 Water bridges: F:S.184 FMT.36: 3 residues within 4Å: Chain E: R.100 Chain F: M.213, K.214 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Water bridges: F:K.214 Hydrogen bonds: E:R.100

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

SAM dependent methyltransferase

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