SMTL ID : 4f86.1 (1 other biounit)

Structure analysis of Geranyl diphosphate methyltransferase in complex with GPP and sinefungin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

6 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 22 residues within 4Å: Chain A: Q.50, I.53, W.57, H.77, H.78, D.131, G.133, C.134, G.135, S.139, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.77 Hydrogen bonds: A:Q.50, A:H.77, A:G.133, A:G.135, A:S.139, A:T.155, A:L.156, A:Q.160, A:Q.160, A:N.183, A:M.184, A:N.200, A:N.200, A:N.200 Salt bridges: A:H.78 SFG.4: 22 residues within 4Å: Chain B: Q.50, W.57, H.77, H.78, D.131, G.133, C.134, G.135, S.139, V.154, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.77 Hydrogen bonds: B:Q.50, B:W.57, B:H.77, B:H.77, B:G.133, B:G.135, B:S.139, B:T.155, B:L.156, B:Q.160, B:N.183, B:M.184, B:N.200, B:N.200 Salt bridges: B:H.78 SFG.7: 20 residues within 4Å: Chain C: W.57, H.77, H.78, D.131, G.133, C.134, G.135, V.154, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:H.77 Hydrogen bonds: C:H.77, C:H.77, C:G.133, C:G.135, C:L.156, C:Q.160, C:N.183, C:M.184, C:N.200, C:N.200 Salt bridges: C:H.78 SFG.10: 20 residues within 4Å: Chain D: Q.50, W.57, H.77, H.78, D.131, G.133, C.134, G.135, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.11 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:H.77 Hydrogen bonds: D:W.57, D:H.77, D:G.133, D:G.135, D:L.156, D:Q.160, D:N.183, D:M.184, D:N.200, D:E.201 Salt bridges: D:H.78 SFG.13: 22 residues within 4Å: Chain E: Q.50, I.53, W.57, H.77, H.78, D.131, G.133, C.134, G.135, S.139, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.14 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:H.77 Hydrogen bonds: E:W.57, E:H.77, E:H.77, E:G.133, E:G.135, E:S.139, E:L.156, E:Q.160, E:N.183, E:M.184, E:N.200, E:N.200 Salt bridges: E:H.78 SFG.16: 23 residues within 4Å: Chain F: I.53, W.57, Y.75, H.76, H.77, H.78, G.133, C.134, G.135, S.139, V.154, T.155, L.156, Q.160, C.182, N.183, M.184, N.200, E.201, S.202, Y.205, V.206 Ligands: GPP.17 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:W.57, F:H.77, F:Y.205 Hydrogen bonds: F:H.77, F:G.133, F:C.134, F:G.135, F:T.155, F:L.156, F:Q.160, F:Q.160, F:N.183, F:M.184, F:E.201 Salt bridges: F:H.78

6 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.2: 18 residues within 4Å: Chain A: W.57, E.60, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, F.250, I.254, R.288, T.295, F.301 Ligands: SFG.1, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.57, A:Y.205, A:F.250, A:I.254, A:F.301 Hydrogen bonds: A:N.65, A:N.65, A:H.77, A:T.295 Salt bridges: A:R.62, A:R.62, A:H.77, A:R.288 GPP.5: 17 residues within 4Å: Chain B: Y.56, W.57, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, G.230, F.250, R.288, T.295 Ligands: SFG.4, MG.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.57, B:E.201, B:F.250 Hydrogen bonds: B:N.65, B:N.65 Salt bridges: B:H.77, B:R.288 GPP.8: 20 residues within 4Å: Chain C: W.57, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, T.229, G.230, I.246, F.250, R.288, T.295, F.301, F.310 Ligands: SFG.7, MG.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.57, C:Y.79, C:E.201, C:Y.205, C:I.246, C:F.250, C:F.301 Hydrogen bonds: C:N.65, C:N.65, C:H.77, C:Y.79 Salt bridges: C:R.62, C:H.77, C:R.288 GPP.11: 17 residues within 4Å: Chain D: W.57, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, F.250, R.288, T.295, F.301, F.310 Ligands: SFG.10, MG.12 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.79, D:E.201, D:F.250, D:F.301, D:F.301, D:F.310 Hydrogen bonds: D:N.65, D:N.65, D:H.77, D:Y.79 Salt bridges: D:R.62, D:R.62, D:H.77, D:R.288 GPP.14: 15 residues within 4Å: Chain E: W.57, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, F.250, R.288, T.295 Ligands: SFG.13, MG.15 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:W.57, E:W.57, E:Y.79, E:E.201, E:Y.205, E:F.250, E:F.250 Hydrogen bonds: E:N.65, E:N.65, E:H.77, E:Y.79 Salt bridges: E:R.62, E:R.62, E:H.77, E:R.288 GPP.17: 18 residues within 4Å: Chain F: W.57, R.62, V.64, N.65, H.77, H.78, Y.79, E.201, M.204, Y.205, G.230, F.250, I.254, R.288, F.301, F.310 Ligands: SFG.16, MG.18 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:W.57, F:F.250, F:I.254, F:F.301, F:F.310 Hydrogen bonds: F:N.65, F:N.65, F:H.77 Salt bridges: F:R.62, F:R.62, F:H.77, F:R.288

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: V.64, N.65, H.78, E.109, Y.284 Ligands: GPP.2 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain B: V.64, N.65, H.78, E.109, Y.284 Ligands: GPP.5 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain C: V.64, N.65, H.78, E.109, Y.284, R.288 Ligands: GPP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.109 MG.12: 5 residues within 4Å: Chain D: N.65, H.78, E.109, Y.284 Ligands: GPP.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.78, D:E.109, D:E.109 MG.15: 5 residues within 4Å: Chain E: N.65, H.78, E.109, Y.284 Ligands: GPP.14 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain F: N.65, H.78, E.109 Ligands: GPP.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ariyawutthiphan, O. et al., Structure analysis of geranyl pyrophosphate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation. Acta Crystallogr.,Sect.D (2012)

Release Date

2012-10-31

Peptides

Geranyl diphosphate 2-C-methyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Geranyl diphosphate 2-C-methyltransferase

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