SMTL ID : 6qlv.1

Crystal structure of W200H UbiX in complex with a geranyl-FMN N5 adduct

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-12-mer

Ligands

9 x HZZ: [(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate(Non-covalent)

HZZ.1: 11 residues within 4Å: Chain A: W.105, A.110, S.111, G.112, R.143, K.150 Chain E: Y.190, R.206 Chain J: R.160, E.161 Ligands: FMN.31 12 PLIP interactions: 4 interactions with chain A, 5 interactions with chain J, 3 interactions with chain E Hydrogen bonds: A:G.112, J:E.161, J:A.162, E:Y.190, E:R.206 Water bridges: A:S.113, J:A.162, J:A.162 Salt bridges: A:R.143, A:K.150, J:R.160 Hydrophobic interactions: E:Y.190 HZZ.5: 11 residues within 4Å: Chain B: W.105, A.110, S.111, G.112, R.143, K.150 Chain E: R.160, E.161 Chain J: Y.190, R.206 Ligands: FMN.14 13 PLIP interactions: 5 interactions with chain B, 4 interactions with chain E, 4 interactions with chain J Hydrogen bonds: B:G.112, E:E.161, E:E.161, J:Y.190 Water bridges: B:S.113, B:S.113, E:A.162 Salt bridges: B:R.143, B:K.150, E:R.160, J:R.206 Hydrophobic interactions: J:Y.190, J:Y.190 HZZ.7: 10 residues within 4Å: Chain A: Y.190 Chain C: W.105, A.110, S.111, G.112, R.143, K.150 Chain H: R.160, E.161 Ligands: FMN.24 12 PLIP interactions: 4 interactions with chain H, 4 interactions with chain A, 4 interactions with chain C Hydrogen bonds: H:E.161, A:Y.190, C:G.112 Water bridges: H:R.160, H:A.162, C:S.113 Salt bridges: H:R.160, C:R.143, C:K.150 Hydrophobic interactions: A:Y.190, A:Y.190, A:Y.190 HZZ.20: 10 residues within 4Å: Chain G: W.105, A.110, S.111, G.112, R.143, K.150 Chain K: R.160, E.161 Chain L: Y.190 Ligands: FMN.36 11 PLIP interactions: 3 interactions with chain L, 3 interactions with chain K, 5 interactions with chain G Hydrophobic interactions: L:Y.190, L:Y.190, G:A.110 Water bridges: L:Y.190, K:R.160, G:S.113 Hydrogen bonds: K:E.161, G:G.112 Salt bridges: K:R.160, G:R.143, G:K.150 HZZ.25: 11 residues within 4Å: Chain D: T.69, R.160, E.161 Chain G: Y.190 Chain H: W.105, A.110, S.111, G.112, R.143, K.150 Ligands: FMN.12 12 PLIP interactions: 4 interactions with chain H, 2 interactions with chain G, 6 interactions with chain D Hydrogen bonds: H:G.112, D:E.161, D:E.161 Water bridges: H:S.113, G:Y.190, D:R.160, D:A.162 Salt bridges: H:R.143, H:K.150, D:R.160 Hydrophobic interactions: G:Y.190, D:T.69 HZZ.28: 11 residues within 4Å: Chain B: R.160, E.161 Chain F: Y.190 Chain I: W.105, M.106, A.110, S.111, G.112, R.143, K.150 Ligands: FMN.3 10 PLIP interactions: 4 interactions with chain I, 2 interactions with chain F, 4 interactions with chain B Hydrogen bonds: I:G.112, F:Y.190, B:E.161 Water bridges: I:S.113, F:R.206, B:R.160, B:A.162 Salt bridges: I:R.143, I:K.150, B:R.160 HZZ.33: 11 residues within 4Å: Chain J: W.105, M.106, A.110, S.111, G.112, R.143, K.150 Chain K: Y.190 Chain L: R.160, E.161 Ligands: FMN.37 8 PLIP interactions: 3 interactions with chain J, 3 interactions with chain L, 2 interactions with chain K Hydrogen bonds: J:G.112, L:E.161 Salt bridges: J:R.143, J:K.150, L:R.160 Water bridges: L:A.162, K:R.206, K:R.206 HZZ.35: 11 residues within 4Å: Chain B: Y.190 Chain F: R.160, E.161 Chain K: W.105, M.106, A.110, S.111, G.112, R.143, K.150 Ligands: FMN.16 11 PLIP interactions: 2 interactions with chain B, 5 interactions with chain F, 4 interactions with chain K Hydrophobic interactions: B:Y.190 Water bridges: B:Y.190, F:A.162, F:A.162, K:S.113 Hydrogen bonds: F:E.161, F:E.161, K:G.112 Salt bridges: F:R.160, K:R.143, K:K.150 HZZ.38: 10 residues within 4Å: Chain A: R.160, E.161 Chain H: Y.190 Chain L: W.105, A.110, S.111, G.112, R.143, K.150 Ligands: FMN.2 10 PLIP interactions: 5 interactions with chain A, 4 interactions with chain L, 1 interactions with chain H Hydrogen bonds: A:E.161, A:E.161, L:G.112 Water bridges: A:A.162, A:A.162, L:S.113, H:Y.190 Salt bridges: A:R.160, L:R.143, L:K.150

9 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 17 residues within 4Å: Chain A: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Chain L: W.105, C.137, R.143 Ligands: HZZ.38 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain L Hydrophobic interactions: A:L.65, A:V.66, L:W.105 Hydrogen bonds: A:G.34, A:G.34, A:S.36, A:S.60, A:S.125, A:S.125, A:T.126, A:T.128, A:T.128, A:R.160, A:R.160, A:E.161, L:R.143 Water bridges: A:K.61, A:A.62, A:G.127, A:T.128, A:E.142, A:R.160 FMN.3: 17 residues within 4Å: Chain B: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Chain I: W.105, C.137, R.143 Ligands: HZZ.28 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain I Hydrophobic interactions: B:L.65, B:V.66, I:W.105 Hydrogen bonds: B:G.34, B:G.34, B:S.36, B:S.60, B:S.125, B:S.125, B:T.126, B:T.128, B:R.160, B:R.160, B:E.161, I:R.143 Water bridges: B:A.62, B:A.62, B:G.127, B:T.128, B:E.142, B:E.142, B:R.160 FMN.12: 17 residues within 4Å: Chain D: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Chain H: W.105, C.137, R.143 Ligands: HZZ.25 24 PLIP interactions: 21 interactions with chain D, 3 interactions with chain H Hydrophobic interactions: D:L.65, D:V.66, H:W.105 Hydrogen bonds: D:G.34, D:G.34, D:S.36, D:S.60, D:S.125, D:S.125, D:T.126, D:T.128, D:T.128, D:R.160, D:R.160, D:E.161, H:R.143 Water bridges: D:A.62, D:A.62, D:G.127, D:T.128, D:N.139, D:E.142, D:R.160, H:N.138 FMN.14: 17 residues within 4Å: Chain B: W.105, C.137, R.143 Chain E: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: HZZ.5 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.65, E:V.66, B:W.105 Hydrogen bonds: E:G.34, E:G.34, E:S.36, E:S.60, E:S.125, E:S.125, E:T.126, E:T.128, E:T.128, E:R.160, E:R.160, E:E.161, B:R.143 Water bridges: E:A.62, E:A.62, E:S.125, E:G.127, E:N.139, E:E.142, E:R.160 FMN.16: 17 residues within 4Å: Chain F: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Chain K: W.105, C.137, R.143 Ligands: HZZ.35 24 PLIP interactions: 22 interactions with chain F, 2 interactions with chain K Hydrophobic interactions: F:L.65, F:V.66, K:W.105 Hydrogen bonds: F:G.34, F:G.34, F:S.36, F:S.60, F:S.60, F:S.125, F:S.125, F:T.126, F:T.128, F:T.128, F:R.160, F:R.160, K:R.143 Water bridges: F:A.62, F:A.62, F:A.62, F:G.127, F:N.139, F:E.142, F:E.142, F:R.160 FMN.24: 17 residues within 4Å: Chain C: W.105, C.137, R.143 Chain H: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: HZZ.7 22 PLIP interactions: 20 interactions with chain H, 2 interactions with chain C Hydrophobic interactions: H:L.65, H:V.66, C:W.105 Hydrogen bonds: H:G.34, H:G.34, H:S.36, H:S.60, H:S.60, H:S.125, H:S.125, H:T.126, H:T.128, H:R.160, H:R.160, H:E.161, C:R.143 Water bridges: H:A.62, H:A.62, H:A.62, H:G.127, H:G.127, H:R.160 FMN.31: 17 residues within 4Å: Chain A: W.105, C.137, R.143 Chain J: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: HZZ.1 22 PLIP interactions: 2 interactions with chain A, 20 interactions with chain J Hydrophobic interactions: A:W.105, J:L.65, J:V.66 Hydrogen bonds: A:R.143, J:G.34, J:G.34, J:S.36, J:S.60, J:S.60, J:S.125, J:S.125, J:T.126, J:T.128, J:R.160, J:R.160 Water bridges: J:A.62, J:A.62, J:G.127, J:N.139, J:E.142, J:E.142, J:R.160 FMN.36: 17 residues within 4Å: Chain G: W.105, C.137, R.143 Chain K: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: HZZ.20 21 PLIP interactions: 2 interactions with chain G, 19 interactions with chain K Hydrophobic interactions: G:W.105, K:L.65, K:V.66 Hydrogen bonds: G:R.143, K:G.34, K:G.34, K:S.36, K:S.60, K:S.60, K:S.125, K:T.126, K:T.128, K:T.128, K:R.160, K:R.160, K:E.161 Water bridges: K:A.62, K:A.62, K:G.127, K:N.139, K:R.160 FMN.37: 18 residues within 4Å: Chain J: W.105, M.106, C.137, R.143 Chain L: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: HZZ.33 22 PLIP interactions: 20 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:L.65, L:V.66, J:W.105 Hydrogen bonds: L:G.34, L:G.34, L:S.36, L:S.60, L:S.125, L:S.125, L:T.126, L:T.128, L:R.160, L:R.160, L:E.161, J:R.143 Water bridges: L:A.62, L:A.62, L:G.127, L:T.128, L:N.139, L:E.142, L:R.160

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain B: S.60, K.61, Q.102, N.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.61, B:Q.102, B:N.139 ACT.8: 5 residues within 4Å: Chain C: V.49, E.52, C.90, G.91, Q.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.91 ACT.17: 3 residues within 4Å: Chain F: S.60, K.61, Q.102 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Q.102 Hydrogen bonds: F:K.61, F:Q.102, F:N.139 Water bridges: F:A.62 ACT.21: 3 residues within 4Å: Chain G: S.60, K.61, Q.102 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:Q.102 Hydrogen bonds: G:K.61, G:Q.102 Water bridges: G:A.62, G:N.139 ACT.26: 4 residues within 4Å: Chain H: S.60, K.61, Q.102, N.139 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:Q.102 Hydrogen bonds: H:K.61, H:Q.102, H:N.139 Water bridges: H:A.62 ACT.29: 4 residues within 4Å: Chain I: S.60, K.61, Q.102, N.139 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:Q.102 Hydrogen bonds: I:K.61, I:Q.102, I:N.139 Salt bridges: I:K.61 ACT.32: 4 residues within 4Å: Chain J: S.60, K.61, Q.102, N.139 4 PLIP interactions: 4 interactions with chain J Hydrogen bonds: J:K.61, J:Q.102 Water bridges: J:S.60, J:A.62

7 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain B: N.138 Chain E: E.142 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.136 Water bridges: B:N.138 NA.10: 2 residues within 4Å: Chain C: N.138 Chain H: E.142 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain C Hydrogen bonds: H:N.139, C:N.138, C:N.138 NA.11: 2 residues within 4Å: Chain C: E.142 Chain D: N.138 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.138, D:N.138 NA.18: 3 residues within 4Å: Chain F: A.136, N.138 Chain G: E.142 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.142 NA.23: 2 residues within 4Å: Chain G: N.138 Chain K: E.142 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain K Water bridges: G:N.138, G:N.138 Hydrogen bonds: K:E.142 NA.27: 2 residues within 4Å: Chain B: E.142 Chain I: N.138 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain I Hydrogen bonds: B:E.142 Water bridges: I:N.138, I:N.138 NA.34: 2 residues within 4Å: Chain J: N.138 Chain L: E.142 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.138 Water bridges: J:N.138

3 x HJN: [(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2,6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate(Non-covalent)

HJN.9: 21 residues within 4Å: Chain C: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Chain D: W.105, M.106, A.110, S.111, C.137, R.143 Chain I: Y.190 Ligands: PO4.13 28 PLIP interactions: 20 interactions with chain C, 7 interactions with chain D, 1 interactions with chain I Hydrophobic interactions: C:L.65, C:V.66, D:W.105, D:A.110, I:Y.190 Hydrogen bonds: C:G.34, C:G.34, C:S.36, C:S.60, C:S.60, C:S.125, C:T.126, C:T.128, C:T.128, C:R.160, C:R.160, D:C.137, D:R.143 Water bridges: C:A.62, C:A.62, C:S.125, C:G.127, C:G.127, C:E.142, C:E.142, D:C.137, D:N.138 pi-Cation interactions: D:R.143 HJN.22: 21 residues within 4Å: Chain D: Y.190 Chain F: W.105, M.106, A.110, S.111, C.137, R.143 Chain G: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.19 28 PLIP interactions: 20 interactions with chain G, 2 interactions with chain D, 6 interactions with chain F Hydrophobic interactions: G:L.65, G:V.66, D:Y.190, D:Y.190, F:W.105 Hydrogen bonds: G:G.34, G:G.34, G:S.36, G:S.60, G:S.60, G:S.125, G:T.126, G:T.128, G:R.160, G:R.160, F:C.137, F:R.143 Water bridges: G:K.61, G:A.62, G:G.127, G:G.127, G:G.127, G:E.142, G:E.142, G:E.142, F:C.137, F:N.138 pi-Cation interactions: F:R.143 HJN.30: 21 residues within 4Å: Chain C: Y.190 Chain E: W.105, A.110, S.111, C.137, R.143 Chain I: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, T.69, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.15 31 PLIP interactions: 5 interactions with chain E, 23 interactions with chain I, 3 interactions with chain C Hydrophobic interactions: E:W.105, I:L.65, I:V.66, I:T.69, C:Y.190, C:Y.190, C:Y.190 Hydrogen bonds: E:C.137, E:R.143, I:G.34, I:G.34, I:S.36, I:S.60, I:S.60, I:S.125, I:T.126, I:T.128, I:T.128, I:R.160, I:R.160 Water bridges: E:C.137, I:A.62, I:A.62, I:G.127, I:G.127, I:G.127, I:N.139, I:E.142, I:E.142, I:R.160 pi-Cation interactions: E:R.143

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 8 residues within 4Å: Chain C: R.160, E.161 Chain D: S.111, G.112, R.143, K.150 Chain I: Y.190 Ligands: HJN.9 8 PLIP interactions: 2 interactions with chain C, 5 interactions with chain D, 1 interactions with chain I Water bridges: C:A.162, D:S.113, D:S.113 Salt bridges: C:R.160, D:R.143, D:K.150 Hydrogen bonds: D:G.112, I:Y.190 PO4.15: 8 residues within 4Å: Chain C: Y.190 Chain E: S.111, G.112, R.143, K.150 Chain I: R.160, E.161 Ligands: HJN.30 12 PLIP interactions: 5 interactions with chain I, 2 interactions with chain C, 5 interactions with chain E Hydrogen bonds: I:E.161, I:E.161, C:Y.190, E:S.111, E:G.112 Water bridges: I:A.162, I:A.162, C:R.206, E:S.113 Salt bridges: I:R.160, E:R.143, E:K.150 PO4.19: 8 residues within 4Å: Chain D: Y.190 Chain F: S.111, G.112, R.143, K.150 Chain G: R.160, E.161 Ligands: HJN.22 10 PLIP interactions: 5 interactions with chain F, 3 interactions with chain G, 2 interactions with chain D Hydrogen bonds: F:G.112, G:E.161, D:Y.190, D:R.206 Water bridges: F:S.113, F:S.113, G:A.162 Salt bridges: F:R.143, F:K.150, G:R.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marshall, S.A. et al., The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun (2019)

Release Date

2019-06-05

Peptides

Flavin prenyltransferase UbiX: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Flavin prenyltransferase UbiX