- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.56 Å
- Oligo State
- homo-36-mer
- Ligands
- 36 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 36 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
SAH.2: 17 residues within 4Å:- Chain A: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.1
17 PLIP interactions:17 interactions with chain A- Hydrogen bonds: A:Y.47, A:G.102, A:G.102, A:G.104, A:N.125, A:N.125, A:D.152, A:D.152, A:A.153, A:I.169
- Water bridges: A:G.108, A:G.108, A:T.124, A:H.129, A:I.169
- Salt bridges: A:H.48
- pi-Stacking: A:F.175
SAH.3: 19 residues within 4Å:- Chain B: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.4
11 PLIP interactions:11 interactions with chain B- Hydrogen bonds: B:Y.47, B:G.102, B:G.104, B:N.125, B:N.125, B:D.152, B:A.153
- Water bridges: B:G.108, B:I.169
- Salt bridges: B:H.48
- pi-Stacking: B:F.175
SAH.5: 18 residues within 4Å:- Chain C: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain C- Hydrogen bonds: C:Y.47, C:G.102, C:G.102, C:G.104, C:T.124, C:N.125, C:D.152, C:D.152, C:A.153
- Water bridges: C:R.22, C:C.103, C:G.106, C:G.108
- Salt bridges: C:H.48
- pi-Stacking: C:F.175
SAH.8: 17 residues within 4Å:- Chain D: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.7
17 PLIP interactions:17 interactions with chain D- Hydrogen bonds: D:Y.47, D:G.102, D:G.102, D:G.104, D:N.125, D:N.125, D:D.152, D:D.152, D:A.153, D:I.169
- Water bridges: D:G.108, D:G.108, D:T.124, D:H.129, D:I.169
- Salt bridges: D:H.48
- pi-Stacking: D:F.175
SAH.9: 19 residues within 4Å:- Chain E: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.10
11 PLIP interactions:11 interactions with chain E- Hydrogen bonds: E:Y.47, E:G.102, E:G.104, E:N.125, E:N.125, E:D.152, E:A.153
- Water bridges: E:G.108, E:I.169
- Salt bridges: E:H.48
- pi-Stacking: E:F.175
SAH.11: 18 residues within 4Å:- Chain F: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain F- Hydrogen bonds: F:Y.47, F:G.102, F:G.102, F:G.104, F:T.124, F:N.125, F:D.152, F:D.152, F:A.153
- Water bridges: F:R.22, F:C.103, F:G.106, F:G.108
- Salt bridges: F:H.48
- pi-Stacking: F:F.175
SAH.14: 17 residues within 4Å:- Chain G: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.13
15 PLIP interactions:15 interactions with chain G- Hydrogen bonds: G:Y.47, G:G.102, G:G.102, G:G.104, G:T.124, G:N.125, G:N.125, G:D.152, G:A.153, G:I.169
- Water bridges: G:G.108, G:G.108, G:I.169
- Salt bridges: G:H.48
- pi-Stacking: G:F.175
SAH.15: 19 residues within 4Å:- Chain H: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.16
12 PLIP interactions:12 interactions with chain H- Hydrogen bonds: H:Y.47, H:G.102, H:G.104, H:T.124, H:N.125, H:N.125, H:D.152, H:A.153
- Water bridges: H:G.108, H:I.169
- Salt bridges: H:H.48
- pi-Stacking: H:F.175
SAH.17: 18 residues within 4Å:- Chain I: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain I- Hydrogen bonds: I:Y.47, I:G.102, I:G.102, I:G.104, I:N.125, I:D.152, I:A.153
- Water bridges: I:C.103, I:G.106, I:G.108
- Salt bridges: I:H.48
- pi-Stacking: I:F.175
SAH.20: 17 residues within 4Å:- Chain J: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.19
15 PLIP interactions:15 interactions with chain J- Hydrogen bonds: J:Y.47, J:G.102, J:G.102, J:G.104, J:T.124, J:N.125, J:N.125, J:D.152, J:A.153, J:I.169
- Water bridges: J:G.108, J:G.108, J:I.169
- Salt bridges: J:H.48
- pi-Stacking: J:F.175
SAH.21: 19 residues within 4Å:- Chain K: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.22
12 PLIP interactions:12 interactions with chain K- Hydrogen bonds: K:Y.47, K:G.102, K:G.104, K:T.124, K:N.125, K:N.125, K:D.152, K:A.153
- Water bridges: K:G.108, K:I.169
- Salt bridges: K:H.48
- pi-Stacking: K:F.175
SAH.23: 18 residues within 4Å:- Chain L: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain L- Hydrogen bonds: L:Y.47, L:G.102, L:G.102, L:G.104, L:N.125, L:D.152, L:A.153
- Water bridges: L:C.103, L:G.106, L:G.108
- Salt bridges: L:H.48
- pi-Stacking: L:F.175
SAH.26: 17 residues within 4Å:- Chain M: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.25
17 PLIP interactions:17 interactions with chain M- Hydrogen bonds: M:Y.47, M:G.102, M:G.102, M:G.104, M:N.125, M:N.125, M:D.152, M:D.152, M:A.153, M:I.169
- Water bridges: M:G.108, M:G.108, M:T.124, M:H.129, M:I.169
- Salt bridges: M:H.48
- pi-Stacking: M:F.175
SAH.27: 19 residues within 4Å:- Chain N: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.28
11 PLIP interactions:11 interactions with chain N- Hydrogen bonds: N:Y.47, N:G.102, N:G.104, N:N.125, N:N.125, N:D.152, N:A.153
- Water bridges: N:G.108, N:I.169
- Salt bridges: N:H.48
- pi-Stacking: N:F.175
SAH.29: 18 residues within 4Å:- Chain O: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain O- Hydrogen bonds: O:Y.47, O:G.102, O:G.102, O:G.104, O:T.124, O:N.125, O:D.152, O:D.152, O:A.153
- Water bridges: O:R.22, O:C.103, O:G.106, O:G.108
- Salt bridges: O:H.48
- pi-Stacking: O:F.175
SAH.32: 17 residues within 4Å:- Chain P: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.31
17 PLIP interactions:17 interactions with chain P- Hydrogen bonds: P:Y.47, P:G.102, P:G.102, P:G.104, P:N.125, P:N.125, P:D.152, P:D.152, P:A.153, P:I.169
- Water bridges: P:G.108, P:G.108, P:T.124, P:H.129, P:I.169
- Salt bridges: P:H.48
- pi-Stacking: P:F.175
SAH.33: 19 residues within 4Å:- Chain Q: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.34
11 PLIP interactions:11 interactions with chain Q- Hydrogen bonds: Q:Y.47, Q:G.102, Q:G.104, Q:N.125, Q:N.125, Q:D.152, Q:A.153
- Water bridges: Q:G.108, Q:I.169
- Salt bridges: Q:H.48
- pi-Stacking: Q:F.175
SAH.35: 18 residues within 4Å:- Chain R: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain R- Hydrogen bonds: R:Y.47, R:G.102, R:G.102, R:G.104, R:T.124, R:N.125, R:D.152, R:D.152, R:A.153
- Water bridges: R:R.22, R:C.103, R:G.106, R:G.108
- Salt bridges: R:H.48
- pi-Stacking: R:F.175
SAH.38: 17 residues within 4Å:- Chain S: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.37
15 PLIP interactions:15 interactions with chain S- Hydrogen bonds: S:Y.47, S:G.102, S:G.102, S:G.104, S:T.124, S:N.125, S:N.125, S:D.152, S:A.153, S:I.169
- Water bridges: S:G.108, S:G.108, S:I.169
- Salt bridges: S:H.48
- pi-Stacking: S:F.175
SAH.39: 19 residues within 4Å:- Chain T: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.40
12 PLIP interactions:12 interactions with chain T- Hydrogen bonds: T:Y.47, T:G.102, T:G.104, T:T.124, T:N.125, T:N.125, T:D.152, T:A.153
- Water bridges: T:G.108, T:I.169
- Salt bridges: T:H.48
- pi-Stacking: T:F.175
SAH.41: 18 residues within 4Å:- Chain U: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain U- Hydrogen bonds: U:Y.47, U:G.102, U:G.102, U:G.104, U:N.125, U:D.152, U:A.153
- Water bridges: U:C.103, U:G.106, U:G.108
- Salt bridges: U:H.48
- pi-Stacking: U:F.175
SAH.44: 17 residues within 4Å:- Chain V: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.43
15 PLIP interactions:15 interactions with chain V- Hydrogen bonds: V:Y.47, V:G.102, V:G.102, V:G.104, V:T.124, V:N.125, V:N.125, V:D.152, V:A.153, V:I.169
- Water bridges: V:G.108, V:G.108, V:I.169
- Salt bridges: V:H.48
- pi-Stacking: V:F.175
SAH.45: 19 residues within 4Å:- Chain W: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.46
12 PLIP interactions:12 interactions with chain W- Hydrogen bonds: W:Y.47, W:G.102, W:G.104, W:T.124, W:N.125, W:N.125, W:D.152, W:A.153
- Water bridges: W:G.108, W:I.169
- Salt bridges: W:H.48
- pi-Stacking: W:F.175
SAH.47: 18 residues within 4Å:- Chain X: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain X- Hydrogen bonds: X:Y.47, X:G.102, X:G.102, X:G.104, X:N.125, X:D.152, X:A.153
- Water bridges: X:C.103, X:G.106, X:G.108
- Salt bridges: X:H.48
- pi-Stacking: X:F.175
SAH.50: 17 residues within 4Å:- Chain Y: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.49
17 PLIP interactions:17 interactions with chain Y- Hydrogen bonds: Y:Y.47, Y:G.102, Y:G.102, Y:G.104, Y:N.125, Y:N.125, Y:D.152, Y:D.152, Y:A.153, Y:I.169
- Water bridges: Y:G.108, Y:G.108, Y:T.124, Y:H.129, Y:I.169
- Salt bridges: Y:H.48
- pi-Stacking: Y:F.175
SAH.51: 19 residues within 4Å:- Chain Z: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.52
11 PLIP interactions:11 interactions with chain Z- Hydrogen bonds: Z:Y.47, Z:G.102, Z:G.104, Z:N.125, Z:N.125, Z:D.152, Z:A.153
- Water bridges: Z:G.108, Z:I.169
- Salt bridges: Z:H.48
- pi-Stacking: Z:F.175
SAH.53: 18 residues within 4Å:- Chain 0: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain 0- Hydrogen bonds: 0:Y.47, 0:G.102, 0:G.102, 0:G.104, 0:T.124, 0:N.125, 0:D.152, 0:D.152, 0:A.153
- Water bridges: 0:R.22, 0:C.103, 0:G.106, 0:G.108
- Salt bridges: 0:H.48
- pi-Stacking: 0:F.175
SAH.56: 17 residues within 4Å:- Chain 1: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.55
17 PLIP interactions:17 interactions with chain 1- Hydrogen bonds: 1:Y.47, 1:G.102, 1:G.102, 1:G.104, 1:N.125, 1:N.125, 1:D.152, 1:D.152, 1:A.153, 1:I.169
- Water bridges: 1:G.108, 1:G.108, 1:T.124, 1:H.129, 1:I.169
- Salt bridges: 1:H.48
- pi-Stacking: 1:F.175
SAH.57: 19 residues within 4Å:- Chain 2: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.58
11 PLIP interactions:11 interactions with chain 2- Hydrogen bonds: 2:Y.47, 2:G.102, 2:G.104, 2:N.125, 2:N.125, 2:D.152, 2:A.153
- Water bridges: 2:G.108, 2:I.169
- Salt bridges: 2:H.48
- pi-Stacking: 2:F.175
SAH.59: 18 residues within 4Å:- Chain 3: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
15 PLIP interactions:15 interactions with chain 3- Hydrogen bonds: 3:Y.47, 3:G.102, 3:G.102, 3:G.104, 3:T.124, 3:N.125, 3:D.152, 3:D.152, 3:A.153
- Water bridges: 3:R.22, 3:C.103, 3:G.106, 3:G.108
- Salt bridges: 3:H.48
- pi-Stacking: 3:F.175
SAH.62: 17 residues within 4Å:- Chain 4: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.61
15 PLIP interactions:15 interactions with chain 4- Hydrogen bonds: 4:Y.47, 4:G.102, 4:G.102, 4:G.104, 4:T.124, 4:N.125, 4:N.125, 4:D.152, 4:A.153, 4:I.169
- Water bridges: 4:G.108, 4:G.108, 4:I.169
- Salt bridges: 4:H.48
- pi-Stacking: 4:F.175
SAH.63: 19 residues within 4Å:- Chain 5: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.64
12 PLIP interactions:12 interactions with chain 5- Hydrogen bonds: 5:Y.47, 5:G.102, 5:G.104, 5:T.124, 5:N.125, 5:N.125, 5:D.152, 5:A.153
- Water bridges: 5:G.108, 5:I.169
- Salt bridges: 5:H.48
- pi-Stacking: 5:F.175
SAH.65: 18 residues within 4Å:- Chain 6: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain 6- Hydrogen bonds: 6:Y.47, 6:G.102, 6:G.102, 6:G.104, 6:N.125, 6:D.152, 6:A.153
- Water bridges: 6:C.103, 6:G.106, 6:G.108
- Salt bridges: 6:H.48
- pi-Stacking: 6:F.175
SAH.68: 17 residues within 4Å:- Chain 7: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.67
15 PLIP interactions:15 interactions with chain 7- Hydrogen bonds: 7:Y.47, 7:G.102, 7:G.102, 7:G.104, 7:T.124, 7:N.125, 7:N.125, 7:D.152, 7:A.153, 7:I.169
- Water bridges: 7:G.108, 7:G.108, 7:I.169
- Salt bridges: 7:H.48
- pi-Stacking: 7:F.175
SAH.69: 19 residues within 4Å:- Chain 8: V.24, Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
- Ligands: EPE.70
12 PLIP interactions:12 interactions with chain 8- Hydrogen bonds: 8:Y.47, 8:G.102, 8:G.104, 8:T.124, 8:N.125, 8:N.125, 8:D.152, 8:A.153
- Water bridges: 8:G.108, 8:I.169
- Salt bridges: 8:H.48
- pi-Stacking: 8:F.175
SAH.71: 18 residues within 4Å:- Chain 9: Y.28, H.46, Y.47, H.48, G.102, C.103, G.104, T.124, N.125, A.126, C.151, D.152, A.153, I.169, E.170, S.171, Y.174, F.175
12 PLIP interactions:12 interactions with chain 9- Hydrogen bonds: 9:Y.47, 9:G.102, 9:G.102, 9:G.104, 9:N.125, 9:D.152, 9:A.153
- Water bridges: 9:C.103, 9:G.106, 9:G.108
- Salt bridges: 9:H.48
- pi-Stacking: 9:F.175
- 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: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
CG
AH
BI
CJ
AK
BL
CM
AN
BO
CP
AQ
BR
CS
AT
BU
CV
AW
BX
CY
AZ
B0
C1
A2
B3
C4
A5
B6
C7
A8
B9
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.56 Å
- Oligo State
- homo-36-mer
- Ligands
- 36 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 36 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)
- 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: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
AE
BF
CG
AH
BI
CJ
AK
BL
CM
AN
BO
CP
AQ
BR
CS
AT
BU
CV
AW
BX
CY
AZ
B0
C1
A2
B3
C4
A5
B6
C7
A8
B9
C