SMTL ID : 3ou7.3 (2 other biounits)

DhpI-SAM-HEP complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

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

SAM.1: 21 residues within 4Å: Chain A: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.22, A:S.55, A:G.76, A:D.98, A:D.98, A:L.99 Water bridges: A:L.12, A:Y.59, A:W.60, A:A.114 pi-Cation interactions: A:Y.15 SAM.3: 21 residues within 4Å: Chain B: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.54, B:G.56, B:G.76, B:D.98, B:D.98, B:L.99 Water bridges: B:L.12, B:S.55, B:T.57, B:G.58, B:A.114 pi-Cation interactions: B:Y.15 SAM.5: 21 residues within 4Å: Chain C: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:A.54, C:G.56, C:G.76, C:S.77, C:D.98, C:D.98, C:L.99, C:A.114 Water bridges: C:Q.11, C:G.58, C:A.114 SAM.7: 20 residues within 4Å: Chain D: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:A.54, D:A.54, D:G.76, D:S.77, D:D.98, D:D.98, D:L.99 Water bridges: D:Q.11, D:Y.59, D:W.60, D:A.114 pi-Cation interactions: D:Y.15 SAM.9: 21 residues within 4Å: Chain E: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:Y.22, E:Y.22, E:S.55, E:G.76, E:D.98, E:L.99 Water bridges: E:L.12, E:Y.59, E:W.60, E:A.114 pi-Cation interactions: E:Y.15 SAM.11: 21 residues within 4Å: Chain F: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Y.22, F:A.54, F:G.56, F:G.76, F:D.98, F:L.99 Water bridges: F:Q.11, F:S.55, F:T.57, F:G.58, F:A.114 pi-Cation interactions: F:Y.15 SAM.13: 21 residues within 4Å: Chain G: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 Ligands: SO4.14 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:Y.22, G:A.54, G:G.56, G:G.76, G:S.77, G:D.98, G:L.99, G:A.114 Water bridges: G:Q.11, G:E.52, G:G.58 SAM.15: 20 residues within 4Å: Chain H: L.12, Y.15, Y.22, F.26, A.54, S.55, G.56, W.60, D.75, G.76, S.77, M.80, Q.97, D.98, L.99, F.100, A.114, H.115, W.116, H.119 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:Y.22, H:A.54, H:A.54, H:G.76, H:S.77, H:D.98, H:L.99 Water bridges: H:Q.11, H:Y.59, H:W.60, H:A.114, H:H.115 pi-Cation interactions: H:Y.15

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

SO4.2: 8 residues within 4Å: Chain A: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.15, A:R.18 Water bridges: A:R.168, A:K.180, A:K.180 Salt bridges: A:H.119, A:R.168, A:K.180 SO4.4: 8 residues within 4Å: Chain B: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.15, B:R.18 Water bridges: B:K.180, B:K.180 Salt bridges: B:H.119, B:R.168, B:K.180 SO4.6: 8 residues within 4Å: Chain C: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Y.15, C:R.18 Water bridges: C:R.168, C:K.180, C:K.180 Salt bridges: C:H.119, C:R.168, C:K.180 SO4.10: 8 residues within 4Å: Chain E: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.9 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:Y.15, E:Y.15, E:R.18 Water bridges: E:R.168, E:K.180, E:K.180 Salt bridges: E:H.119, E:R.168, E:K.180 SO4.12: 8 residues within 4Å: Chain F: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.11 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:Y.15, F:Y.15, F:R.18 Water bridges: F:K.180, F:K.180 Salt bridges: F:H.119, F:R.168, F:K.180 SO4.14: 8 residues within 4Å: Chain G: Y.15, R.18, V.27, P.28, H.119, R.168, K.180 Ligands: SAM.13 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:Y.15, G:Y.15, G:R.18 Water bridges: G:H.115, G:R.168, G:K.180, G:K.180 Salt bridges: G:H.119, G:R.168, G:K.180

2 x 2HE: (2-hydroxyethyl)phosphonic acid(Non-covalent)

2HE.8: 8 residues within 4Å: Chain D: Y.15, R.18, F.26, V.27, P.28, H.119, R.168, K.180 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Y.15, D:R.18, D:R.18, D:F.26, D:H.119, D:H.119, D:R.168, D:R.168, D:K.180 2HE.16: 8 residues within 4Å: Chain H: Y.15, R.18, F.26, V.27, P.28, H.119, R.168, K.180 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:R.18, H:R.18, H:F.26, H:H.119, H:H.119, H:R.168, H:R.168, H:K.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J.H. et al., Characterization and structure of DhpI, a phosphonate O-methyltransferase involved in dehydrophos biosynthesis. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-10-27

Peptides

SAM-dependent methyltransferase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

SAM-dependent methyltransferase

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