SMTL ID : 6qlg.1

Crystal structure of AnUbiX (PadA1) in complex with FMN and dimethylallyl pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-12-mer

Ligands

12 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.1: 16 residues within 4Å: Chain A: M.106, S.111, S.112, G.113, S.114, R.144, K.151 Chain J: R.161, E.162, T.163 Chain L: A.189, Y.191, Q.203, R.207, W.222 Ligands: FMN.2 16 PLIP interactions: 7 interactions with chain L, 5 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: L:Y.191, L:W.222 Hydrogen bonds: L:Y.191, L:Y.191, L:Q.203, L:R.207, A:G.113, A:S.114, J:R.161 Salt bridges: L:R.207, A:R.144, A:K.151, A:K.151, J:R.161 Water bridges: J:R.161, J:R.161 DMA.4: 15 residues within 4Å: Chain A: A.189, Y.191, Q.203, R.207, W.222 Chain B: R.161, E.162, T.163 Chain E: M.106, S.111, S.112, G.113, R.144, K.151 Ligands: FMN.7 17 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A, 5 interactions with chain E Hydrogen bonds: B:R.161, B:E.162, A:Y.191, A:Q.203, A:R.207, E:G.113, E:S.114 Water bridges: B:R.161, B:R.161 Salt bridges: B:R.161, A:R.207, E:R.144, E:K.151, E:K.151 Hydrophobic interactions: A:Y.191, A:W.222, A:W.222 DMA.8: 15 residues within 4Å: Chain A: R.161, E.162, T.163 Chain B: A.189, Y.191, Q.203, R.207, W.222 Chain C: M.106, S.112, G.113, S.114, R.144, K.151 Ligands: FMN.3 13 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:Y.191, B:W.222 Hydrogen bonds: B:Y.191, B:Q.203, A:T.163, C:S.112, C:G.113, C:R.144 Salt bridges: B:R.207, B:R.207, A:R.161, C:K.151, C:K.151 DMA.9: 15 residues within 4Å: Chain C: A.189, Y.191, Q.203, R.207, W.222 Chain D: M.106, S.111, S.112, G.113, R.144, K.151 Chain I: R.161, E.162, T.163 Ligands: FMN.11 17 PLIP interactions: 5 interactions with chain I, 4 interactions with chain D, 8 interactions with chain C Hydrogen bonds: I:R.161, I:E.162, I:E.162, D:G.113, D:R.144, C:Y.191, C:Y.191, C:Q.203 Water bridges: I:R.161 Salt bridges: I:R.161, D:K.151, D:K.151, C:R.207, C:R.207 Hydrophobic interactions: C:Y.191, C:W.222, C:W.222 DMA.10: 15 residues within 4Å: Chain B: M.106, S.111, S.112, G.113, R.144, K.151 Chain D: A.189, Y.191, Q.203, R.207, W.222 Chain F: R.161, E.162, T.163 Ligands: FMN.14 14 PLIP interactions: 6 interactions with chain D, 4 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: D:Y.191, D:W.222 Hydrogen bonds: D:Y.191, D:Q.203, B:G.113, B:R.144, F:R.161 Salt bridges: D:R.207, D:R.207, B:K.151, B:K.151, F:R.161 Water bridges: F:R.161, F:R.161 DMA.15: 15 residues within 4Å: Chain E: R.161, E.162, T.163 Chain F: M.106, S.111, S.112, G.113, R.144, K.151 Chain K: A.189, Y.191, Q.203, R.207, W.222 Ligands: FMN.13 16 PLIP interactions: 4 interactions with chain F, 6 interactions with chain K, 6 interactions with chain E Hydrogen bonds: F:G.113, F:R.144, K:Y.191, K:Y.191, K:Q.203, E:R.161, E:E.162, E:T.163 Salt bridges: F:K.151, F:K.151, K:R.207, K:R.207, E:R.161 Hydrophobic interactions: K:Y.191 Water bridges: E:R.161, E:R.161 DMA.16: 16 residues within 4Å: Chain D: R.161, E.162, T.163 Chain F: A.189, Y.191, Q.203, R.207, W.222 Chain G: M.106, S.111, S.112, G.113, S.114, R.144, K.151 Ligands: FMN.17 15 PLIP interactions: 6 interactions with chain F, 4 interactions with chain D, 5 interactions with chain G Hydrophobic interactions: F:Y.191, F:W.222 Hydrogen bonds: F:Y.191, F:Q.203, F:R.207, D:R.161, G:G.113, G:S.114 Salt bridges: F:R.207, D:R.161, G:R.144, G:K.151, G:K.151 Water bridges: D:R.161, D:R.161 DMA.19: 15 residues within 4Å: Chain G: A.189, Y.191, Q.203, R.207, W.222 Chain H: R.161, E.162, T.163 Chain K: M.106, S.111, S.112, G.113, R.144, K.151 Ligands: FMN.22 16 PLIP interactions: 6 interactions with chain G, 5 interactions with chain H, 5 interactions with chain K Hydrophobic interactions: G:Y.191, G:W.222, G:W.222 Hydrogen bonds: G:Q.203, G:R.207, H:R.161, H:E.162, K:G.113, K:S.114 Salt bridges: G:R.207, H:R.161, K:R.144, K:K.151, K:K.151 Water bridges: H:R.161, H:R.161 DMA.23: 15 residues within 4Å: Chain G: R.161, E.162, T.163 Chain H: A.189, Y.191, Q.203, R.207, W.222 Chain I: M.106, S.112, G.113, S.114, R.144, K.151 Ligands: FMN.18 12 PLIP interactions: 5 interactions with chain I, 5 interactions with chain H, 2 interactions with chain G Hydrogen bonds: I:S.112, I:G.113, I:R.144, H:Q.203, G:T.163 Salt bridges: I:K.151, I:K.151, H:R.207, H:R.207, G:R.161 Hydrophobic interactions: H:Y.191, H:W.222 DMA.24: 15 residues within 4Å: Chain C: R.161, E.162, T.163 Chain I: A.189, Y.191, Q.203, R.207, W.222 Chain J: M.106, S.111, S.112, G.113, R.144, K.151 Ligands: FMN.26 15 PLIP interactions: 4 interactions with chain C, 7 interactions with chain I, 4 interactions with chain J Hydrogen bonds: C:R.161, C:E.162, I:Y.191, I:Q.203, J:G.113, J:R.144 Water bridges: C:R.161 Salt bridges: C:R.161, I:R.207, I:R.207, J:K.151, J:K.151 Hydrophobic interactions: I:Y.191, I:W.222, I:W.222 DMA.25: 15 residues within 4Å: Chain H: M.106, S.111, S.112, G.113, R.144, K.151 Chain J: A.189, Y.191, Q.203, R.207, W.222 Chain L: R.161, E.162, T.163 Ligands: FMN.29 14 PLIP interactions: 5 interactions with chain J, 5 interactions with chain L, 4 interactions with chain H Hydrophobic interactions: J:Y.191, J:W.222 Hydrogen bonds: J:Q.203, L:R.161, L:E.162, H:G.113, H:R.144 Salt bridges: J:R.207, J:R.207, L:R.161, H:K.151, H:K.151 Water bridges: L:R.161, L:R.161 DMA.30: 15 residues within 4Å: Chain E: A.189, Y.191, Q.203, R.207, W.222 Chain K: R.161, E.162, T.163 Chain L: M.106, S.111, S.112, G.113, R.144, K.151 Ligands: FMN.28 15 PLIP interactions: 6 interactions with chain K, 4 interactions with chain L, 5 interactions with chain E Hydrogen bonds: K:R.161, K:E.162, K:T.163, L:G.113, L:R.144, E:Y.191, E:Q.203 Water bridges: K:R.161, K:R.161 Salt bridges: K:R.161, L:K.151, L:K.151, E:R.207, E:R.207 Hydrophobic interactions: E:Y.191

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain A: M.106, A.107, C.138, D.139, R.144 Chain J: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain L: W.222, W.225 Ligands: DMA.1 20 PLIP interactions: 15 interactions with chain J, 2 interactions with chain L, 3 interactions with chain A Hydrogen bonds: J:G.49, J:G.49, J:T.51, J:S.75, J:S.126, J:M.127, J:T.129, J:R.161, J:R.161, J:E.162, A:R.144, A:R.144 Water bridges: J:K.76, J:K.76, J:S.126, J:K.128 Salt bridges: J:K.128 Hydrophobic interactions: L:W.222, L:W.225, A:A.107 FMN.3: 20 residues within 4Å: Chain A: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain B: W.222, W.225 Chain C: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.8 22 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:G.49, A:G.49, A:T.51, A:S.75, A:S.75, A:S.126, A:M.127, A:T.129, A:T.129, A:R.161, A:R.161, C:R.144, C:R.144, C:R.144 Water bridges: A:K.76, A:W.77, A:K.128 Salt bridges: A:K.128 Hydrophobic interactions: B:W.222, B:W.225, B:W.225, C:A.107 FMN.7: 19 residues within 4Å: Chain A: W.225 Chain B: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain E: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.4 21 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, 4 interactions with chain E Hydrogen bonds: B:G.49, B:G.49, B:T.51, B:S.75, B:S.75, B:S.126, B:M.127, B:T.129, B:T.129, B:R.161, B:R.161, E:R.144, E:R.144, E:R.144 Water bridges: B:K.76, B:W.77, B:K.128 Salt bridges: B:K.128 Hydrophobic interactions: A:W.225, A:W.225, E:A.107 FMN.11: 20 residues within 4Å: Chain C: W.222, W.225 Chain D: M.106, A.107, C.138, D.139, R.144 Chain I: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Ligands: DMA.9 21 PLIP interactions: 15 interactions with chain I, 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: I:G.49, I:G.49, I:T.51, I:S.75, I:S.75, I:S.126, I:M.127, I:T.129, I:R.161, I:R.161, D:R.144, D:R.144 Water bridges: I:K.76, I:W.77, I:S.126, I:K.128 Salt bridges: I:K.128 Hydrophobic interactions: D:A.107, C:W.222, C:W.225, C:W.225 FMN.13: 19 residues within 4Å: Chain E: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain F: M.106, A.107, C.138, D.139, R.144 Chain K: W.222 Ligands: DMA.15 20 PLIP interactions: 15 interactions with chain E, 4 interactions with chain F, 1 interactions with chain K Hydrogen bonds: E:G.49, E:G.49, E:T.51, E:S.75, E:S.75, E:S.126, E:M.127, E:T.129, E:T.129, E:R.161, E:R.161, E:E.162, F:R.144, F:R.144, F:R.144 Water bridges: E:W.77, E:K.128 Salt bridges: E:K.128 Hydrophobic interactions: F:A.107, K:W.222 FMN.14: 20 residues within 4Å: Chain B: M.106, A.107, C.138, D.139, R.144 Chain D: W.222, W.225 Chain F: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Ligands: DMA.10 20 PLIP interactions: 14 interactions with chain F, 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: F:G.49, F:G.49, F:T.51, F:S.75, F:S.126, F:M.127, F:T.129, F:R.161, F:R.161, F:E.162, B:R.144, B:R.144, B:R.144 Water bridges: F:K.76, F:K.76, F:K.128 Salt bridges: F:K.128 Hydrophobic interactions: B:A.107, D:W.222, D:W.225 FMN.17: 20 residues within 4Å: Chain D: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain F: W.222, W.225 Chain G: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.16 20 PLIP interactions: 2 interactions with chain F, 15 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: F:W.222, F:W.225, G:A.107 Hydrogen bonds: D:G.49, D:G.49, D:T.51, D:S.75, D:S.126, D:M.127, D:T.129, D:T.129, D:R.161, D:R.161, G:R.144, G:R.144 Water bridges: D:K.76, D:K.76, D:S.126, D:K.128 Salt bridges: D:K.128 FMN.18: 20 residues within 4Å: Chain G: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain H: W.222, W.225 Chain I: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.23 21 PLIP interactions: 14 interactions with chain G, 3 interactions with chain H, 4 interactions with chain I Hydrogen bonds: G:G.49, G:G.49, G:T.51, G:S.75, G:S.75, G:S.126, G:M.127, G:T.129, G:R.161, G:R.161, I:R.144, I:R.144, I:R.144 Water bridges: G:K.76, G:W.77, G:K.128 Salt bridges: G:K.128 Hydrophobic interactions: H:W.222, H:W.225, H:W.225, I:A.107 FMN.22: 19 residues within 4Å: Chain G: W.225 Chain H: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain K: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.19 21 PLIP interactions: 15 interactions with chain H, 2 interactions with chain G, 4 interactions with chain K Hydrogen bonds: H:G.49, H:G.49, H:T.51, H:S.75, H:S.75, H:S.126, H:M.127, H:T.129, H:R.161, H:R.161, H:E.162, K:R.144, K:R.144, K:R.144 Water bridges: H:K.76, H:W.77, H:K.128 Salt bridges: H:K.128 Hydrophobic interactions: G:W.225, G:W.225, K:A.107 FMN.26: 20 residues within 4Å: Chain C: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain I: W.222, W.225 Chain J: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.24 23 PLIP interactions: 17 interactions with chain C, 3 interactions with chain I, 3 interactions with chain J Hydrogen bonds: C:G.49, C:G.49, C:T.51, C:S.75, C:S.75, C:S.126, C:M.127, C:T.129, C:T.129, C:R.161, C:R.161, C:E.162, J:R.144, J:R.144 Water bridges: C:K.76, C:W.77, C:S.126, C:K.128 Salt bridges: C:K.128 Hydrophobic interactions: I:W.222, I:W.225, I:W.225, J:A.107 FMN.28: 19 residues within 4Å: Chain E: W.222 Chain K: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Chain L: M.106, A.107, C.138, D.139, R.144 Ligands: DMA.30 18 PLIP interactions: 13 interactions with chain K, 4 interactions with chain L, 1 interactions with chain E Hydrogen bonds: K:G.49, K:G.49, K:T.51, K:S.75, K:S.75, K:S.126, K:M.127, K:T.129, K:R.161, K:R.161, L:R.144, L:R.144, L:R.144 Water bridges: K:W.77, K:K.128 Salt bridges: K:K.128 Hydrophobic interactions: L:A.107, E:W.222 FMN.29: 20 residues within 4Å: Chain H: M.106, A.107, C.138, D.139, R.144 Chain J: W.222, W.225 Chain L: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162 Ligands: DMA.25 20 PLIP interactions: 14 interactions with chain L, 2 interactions with chain J, 4 interactions with chain H Hydrogen bonds: L:G.49, L:G.49, L:T.51, L:S.75, L:S.126, L:M.127, L:T.129, L:T.129, L:R.161, L:R.161, H:R.144, H:R.144, H:R.144 Water bridges: L:K.76, L:K.76, L:K.128 Salt bridges: L:K.128 Hydrophobic interactions: J:W.222, J:W.225, H:A.107

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

PO4.5: 2 residues within 4Å: Chain A: K.83, H.89 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.83, A:H.89 PO4.20: 2 residues within 4Å: Chain G: K.83, H.89 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:K.83, G:H.89

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 9 residues within 4Å: Chain A: P.188, F.190, L.200 Chain B: P.186, P.188, F.190, L.200, I.201, S.204 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.204, B:S.204 Water bridges: A:L.200 PEG.12: 7 residues within 4Å: Chain D: P.188, L.200, I.201, S.204 Chain F: P.188, F.190, L.200 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.204, D:S.204 PEG.21: 9 residues within 4Å: Chain G: P.188, F.190, L.200 Chain H: P.186, P.188, F.190, L.200, I.201, S.204 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:S.204, H:S.204 Water bridges: G:L.200 PEG.27: 7 residues within 4Å: Chain J: P.188, L.200, I.201, S.204 Chain L: P.188, F.190, L.200 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:S.204, J:S.204

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 PAD1, mitochondrial: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

E
E

F
F

G
C

H
A

I
B

J
D

K
E

L
F

Flavin prenyltransferase PAD1, mitochondrial