SMTL ID : 7fbh.1

geranyl pyrophosphate C6-methyltransferase BezA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-12-mer

Ligands

12 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 12 residues within 4Å: Chain A: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.39, A:S.252, A:S.252, A:N.281 Water bridges: A:E.170, A:E.198, A:S.277 Salt bridges: A:K.38, A:E.170, A:E.170 EPE.4: 12 residues within 4Å: Chain B: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.39, B:S.252, B:S.252, B:N.281 Water bridges: B:E.170, B:E.198, B:S.277 Salt bridges: B:K.38, B:E.170, B:E.170 EPE.7: 12 residues within 4Å: Chain C: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:E.170, C:S.252, C:S.252, C:N.281 Water bridges: C:E.170, C:E.198, C:S.277 Salt bridges: C:K.38, C:E.170, C:E.170 EPE.10: 12 residues within 4Å: Chain D: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.170, D:S.252, D:S.252, D:N.281 Water bridges: D:E.170, D:E.198, D:S.277 Salt bridges: D:K.38, D:E.170, D:E.170 EPE.14: 12 residues within 4Å: Chain E: K.38, Y.39, Y.47, H.48, E.170, W.210, F.214, F.248, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:E.170, E:E.170, E:S.252, E:N.281 Water bridges: E:Y.47, E:Y.213, E:S.277 Salt bridges: E:K.38, E:E.170, E:E.170 EPE.19: 12 residues within 4Å: Chain F: K.38, Y.39, Y.47, H.48, E.170, W.210, F.214, F.248, W.249, S.252, S.277, N.281 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:E.170, F:E.170, F:S.252, F:N.281 Water bridges: F:Y.47, F:Y.213, F:S.277 Salt bridges: F:K.38, F:E.170, F:E.170 EPE.24: 12 residues within 4Å: Chain G: K.38, Y.39, Y.47, H.48, E.170, W.210, F.214, F.248, W.249, S.252, S.277, N.281 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:Y.39, G:E.170, G:S.252, G:N.281 Water bridges: G:S.277 Salt bridges: G:K.38, G:E.170, G:E.170 EPE.29: 12 residues within 4Å: Chain H: K.38, Y.39, Y.47, H.48, E.170, W.210, F.214, F.248, W.249, S.252, S.277, N.281 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:Y.39, H:E.170, H:S.252, H:N.281 Water bridges: H:S.277 Salt bridges: H:K.38, H:E.170, H:E.170 EPE.34: 12 residues within 4Å: Chain I: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:E.170, I:S.252, I:N.281 Water bridges: I:E.170, I:E.198, I:S.277 Salt bridges: I:K.38, I:E.170, I:E.170 EPE.39: 12 residues within 4Å: Chain J: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:E.170, J:S.252, J:N.281 Water bridges: J:E.170, J:E.198, J:S.277 Salt bridges: J:K.38, J:E.170, J:E.170 EPE.44: 12 residues within 4Å: Chain K: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:Y.39, K:S.252, K:N.281 Water bridges: K:E.170, K:E.198, K:S.277 Salt bridges: K:K.38, K:E.170, K:E.170 EPE.49: 12 residues within 4Å: Chain L: K.38, Y.39, Y.47, H.48, E.170, Y.174, W.210, F.214, W.249, S.252, S.277, N.281 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:Y.39, L:S.252, L:N.281 Water bridges: L:E.170, L:E.198, L:S.277 Salt bridges: L:K.38, L:E.170, L:E.170

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: K.31, Y.213, F.214, Y.215 Chain B: R.272 Ligand excluded by PLIP GOL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: R.272 Chain B: K.31, Y.213, F.214, Y.215 Ligand excluded by PLIP GOL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain C: K.31, Y.213, F.214, Y.215 Chain D: R.272 Ligand excluded by PLIP GOL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain C: R.272 Chain D: K.31, Y.213, F.214, Y.215 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain E: R.59, H.60, T.61, D.63, A.68, F.69, S.72, E.251 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain F: R.59, H.60, T.61, D.63, A.68, F.69, S.72, E.251 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain G: R.59, H.60, T.61, D.63, A.68, F.69, S.72, E.251 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain H: R.59, H.60, T.61, D.63, A.68, F.69, S.72, E.251 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain I: T.202, V.221, D.238, R.294 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain H: P.178, E.226 Chain I: D.63, T.65, D.67, R.71 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain J: T.202, V.221, D.238, R.294 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain G: P.178, E.226 Chain J: D.63, T.65, D.67, R.71 Ligand excluded by PLIP GOL.45: 4 residues within 4Å: Chain K: T.202, V.221, D.238, R.294 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain F: P.178, E.226 Chain K: D.63, T.65, D.67, R.71 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain L: T.202, V.221, D.238, R.294 Ligand excluded by PLIP GOL.52: 6 residues within 4Å: Chain E: P.178, E.226 Chain L: D.63, T.65, D.67, R.71 Ligand excluded by PLIP

8 x LYS: LYSINE(Non-covalent)

LYS.13: 4 residues within 4Å: Chain E: P.190, G.232, E.234, R.302 3 PLIP interactions: 3 interactions with chain E, Hydrophobic interactions: E:P.190 Hydrogen bonds: E:G.232, E:E.234 LYS.18: 4 residues within 4Å: Chain F: P.190, G.232, E.234, R.302 3 PLIP interactions: 3 interactions with chain F, Hydrophobic interactions: F:P.190 Hydrogen bonds: F:G.232, F:E.234 LYS.23: 4 residues within 4Å: Chain G: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain G, Hydrophobic interactions: G:P.190 Hydrogen bonds: G:G.232 LYS.28: 4 residues within 4Å: Chain H: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain H, Hydrophobic interactions: H:P.190 Hydrogen bonds: H:G.232 LYS.33: 4 residues within 4Å: Chain I: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain I, Hydrophobic interactions: I:E.234 Hydrogen bonds: I:R.302 LYS.38: 4 residues within 4Å: Chain J: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain J, Hydrophobic interactions: J:E.234 Hydrogen bonds: J:R.302 LYS.43: 4 residues within 4Å: Chain K: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain K, Hydrophobic interactions: K:E.234 Hydrogen bonds: K:R.302 LYS.48: 4 residues within 4Å: Chain L: P.190, G.232, E.234, R.302 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:E.234 Hydrogen bonds: L:R.302

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

EDO.16: 5 residues within 4Å: Chain C: H.155, L.156 Chain E: D.29, T.32, I.132 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:D.29, C:H.155 EDO.17: 3 residues within 4Å: Chain E: Y.213, Y.215 Chain J: R.272 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:F.214 EDO.21: 5 residues within 4Å: Chain D: H.155, L.156 Chain F: D.29, T.32, I.132 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:H.155, F:D.29 EDO.22: 3 residues within 4Å: Chain F: Y.213, Y.215 Chain I: R.272 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:F.214 EDO.26: 5 residues within 4Å: Chain A: H.155, L.156 Chain G: D.29, T.32, I.132 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:H.155, G:D.29 EDO.27: 3 residues within 4Å: Chain G: Y.213, Y.215 Chain L: R.272 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:F.214 EDO.31: 5 residues within 4Å: Chain B: H.155, L.156 Chain H: D.29, T.32, I.132 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Hydrogen bonds: B:H.155, H:D.29 EDO.32: 3 residues within 4Å: Chain H: Y.213, Y.215 Chain K: R.272 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:F.214 EDO.36: 7 residues within 4Å: Chain I: P.58, H.60, T.61, D.63, F.69, S.72, E.251 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:T.61, I:T.61, I:S.72, I:E.251 Water bridges: I:E.251 EDO.41: 7 residues within 4Å: Chain J: P.58, H.60, T.61, D.63, F.69, S.72, E.251 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:T.61, J:T.61, J:S.72, J:E.251 Water bridges: J:E.251 EDO.46: 7 residues within 4Å: Chain K: P.58, H.60, T.61, D.63, F.69, S.72, E.251 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:T.61, K:T.61, K:S.72, K:E.251 Water bridges: K:H.60 EDO.51: 7 residues within 4Å: Chain L: P.58, H.60, T.61, D.63, F.69, S.72, E.251 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:T.61, L:T.61, L:S.72, L:E.251 Water bridges: L:H.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutsumi, H. et al., Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2021-12-01

Peptides

BezA: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
B

F
B

G
B

H
B

I
C

J
C

K
C

L
C

BezA

Related Entries With Identical Sequence