SMTL ID : 6m8t.1

Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-12-mer

Ligands

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain D: W.188 Chain E: I.73, A.74, A.105, D.106, R.111 24 PLIP interactions: 1 interactions with chain D, 5 interactions with chain E, 18 interactions with chain A Hydrophobic interactions: D:W.188, E:A.74 Hydrogen bonds: E:D.106, A:G.16, A:G.16, A:S.18, A:S.42, A:A.45, A:S.93, A:S.93, A:I.94, A:T.96, A:R.128, A:R.128 Water bridges: E:R.111, E:R.111, E:R.111, A:R.43, A:A.44, A:E.70, A:K.95, A:T.96, A:N.107 Salt bridges: A:K.95 FMN.3: 19 residues within 4Å: Chain B: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain C: W.188 Chain G: I.73, A.74, A.105, D.106, R.111 24 PLIP interactions: 18 interactions with chain B, 5 interactions with chain G, 1 interactions with chain C Hydrogen bonds: B:G.16, B:G.16, B:S.18, B:S.42, B:A.45, B:S.93, B:S.93, B:I.94, B:T.96, B:R.128, B:R.128, G:D.106 Water bridges: B:R.43, B:A.44, B:E.70, B:K.95, B:T.96, B:N.107, G:R.111, G:R.111, G:R.111 Salt bridges: B:K.95 Hydrophobic interactions: G:A.74, C:W.188 FMN.5: 19 residues within 4Å: Chain B: W.188 Chain C: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain H: I.73, A.74, A.105, D.106, R.111 25 PLIP interactions: 19 interactions with chain C, 5 interactions with chain H, 1 interactions with chain B Hydrogen bonds: C:G.16, C:G.16, C:S.18, C:S.42, C:A.45, C:S.93, C:S.93, C:I.94, C:T.96, C:T.96, C:R.128, C:R.128, C:E.129, H:D.106 Water bridges: C:R.43, C:A.44, C:E.70, C:K.95, C:N.107, H:R.111, H:R.111, H:R.111 Salt bridges: C:K.95 Hydrophobic interactions: H:A.74, B:W.188 FMN.7: 19 residues within 4Å: Chain A: W.188 Chain D: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain F: I.73, A.74, A.105, D.106, R.111 25 PLIP interactions: 19 interactions with chain D, 5 interactions with chain F, 1 interactions with chain A Hydrogen bonds: D:G.16, D:G.16, D:S.18, D:S.42, D:A.45, D:S.93, D:S.93, D:I.94, D:T.96, D:T.96, D:R.128, D:R.128, D:E.129, F:D.106 Water bridges: D:R.43, D:A.44, D:E.70, D:K.95, D:N.107, F:R.111, F:R.111, F:R.111 Salt bridges: D:K.95 Hydrophobic interactions: F:A.74, A:W.188 FMN.9: 19 residues within 4Å: Chain E: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain H: W.188 Chain I: I.73, A.74, A.105, D.106, R.111 24 PLIP interactions: 18 interactions with chain E, 5 interactions with chain I, 1 interactions with chain H Hydrogen bonds: E:G.16, E:G.16, E:S.18, E:S.42, E:A.45, E:S.93, E:S.93, E:I.94, E:T.96, E:T.96, E:R.128, E:R.128, I:D.106 Water bridges: E:R.43, E:A.44, E:E.70, E:K.95, E:N.107, I:R.111, I:R.111, I:R.111 Salt bridges: E:K.95 Hydrophobic interactions: I:A.74, H:W.188 FMN.11: 19 residues within 4Å: Chain F: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain G: W.188 Chain K: I.73, A.74, A.105, D.106, R.111 25 PLIP interactions: 19 interactions with chain F, 1 interactions with chain G, 5 interactions with chain K Hydrogen bonds: F:G.16, F:G.16, F:S.18, F:S.42, F:A.45, F:S.93, F:S.93, F:I.94, F:T.96, F:R.128, F:R.128, F:E.129, K:D.106 Water bridges: F:R.43, F:A.44, F:E.70, F:K.95, F:T.96, F:N.107, K:R.111, K:R.111, K:R.111 Salt bridges: F:K.95 Hydrophobic interactions: G:W.188, K:A.74 FMN.13: 19 residues within 4Å: Chain F: W.188 Chain G: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain L: I.73, A.74, A.105, D.106, R.111 24 PLIP interactions: 18 interactions with chain G, 5 interactions with chain L, 1 interactions with chain F Hydrogen bonds: G:G.16, G:G.16, G:S.18, G:S.42, G:A.45, G:S.93, G:S.93, G:I.94, G:T.96, G:T.96, G:R.128, G:R.128, L:D.106 Water bridges: G:R.43, G:A.44, G:E.70, G:K.95, G:N.107, L:R.111, L:R.111, L:R.111 Salt bridges: G:K.95 Hydrophobic interactions: L:A.74, F:W.188 FMN.15: 19 residues within 4Å: Chain E: W.188 Chain H: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain J: I.73, A.74, A.105, D.106, R.111 25 PLIP interactions: 19 interactions with chain H, 5 interactions with chain J, 1 interactions with chain E Hydrogen bonds: H:G.16, H:G.16, H:S.18, H:S.42, H:A.45, H:S.93, H:S.93, H:I.94, H:T.96, H:R.128, H:R.128, H:E.129, J:D.106 Water bridges: H:R.43, H:A.44, H:E.70, H:K.95, H:T.96, H:N.107, J:R.111, J:R.111, J:R.111 Salt bridges: H:K.95 Hydrophobic interactions: J:A.74, E:W.188 FMN.17: 19 residues within 4Å: Chain A: I.73, A.74, A.105, D.106, R.111 Chain I: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain L: W.188 25 PLIP interactions: 19 interactions with chain I, 5 interactions with chain A, 1 interactions with chain L Hydrogen bonds: I:G.16, I:G.16, I:S.18, I:S.42, I:A.45, I:S.93, I:S.93, I:I.94, I:T.96, I:R.128, I:R.128, I:E.129, A:D.106 Water bridges: I:R.43, I:A.44, I:E.70, I:K.95, I:T.96, I:N.107, A:R.111, A:R.111, A:R.111 Salt bridges: I:K.95 Hydrophobic interactions: A:A.74, L:W.188 FMN.19: 19 residues within 4Å: Chain C: I.73, A.74, A.105, D.106, R.111 Chain J: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 Chain K: W.188 24 PLIP interactions: 18 interactions with chain J, 5 interactions with chain C, 1 interactions with chain K Hydrogen bonds: J:G.16, J:G.16, J:S.18, J:S.42, J:A.45, J:S.93, J:S.93, J:I.94, J:T.96, J:T.96, J:R.128, J:R.128, C:D.106 Water bridges: J:R.43, J:A.44, J:E.70, J:K.95, J:N.107, C:R.111, C:R.111, C:R.111 Salt bridges: J:K.95 Hydrophobic interactions: C:A.74, K:W.188 FMN.21: 19 residues within 4Å: Chain D: I.73, A.74, A.105, D.106, R.111 Chain J: W.188 Chain K: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 24 PLIP interactions: 1 interactions with chain J, 18 interactions with chain K, 5 interactions with chain D Hydrophobic interactions: J:W.188, D:A.74 Hydrogen bonds: K:G.16, K:G.16, K:S.18, K:S.42, K:A.45, K:S.93, K:S.93, K:I.94, K:T.96, K:T.96, K:R.128, K:R.128, D:D.106 Water bridges: K:R.43, K:A.44, K:E.70, K:K.95, K:N.107, D:R.111, D:R.111, D:R.111 Salt bridges: K:K.95 FMN.23: 19 residues within 4Å: Chain B: I.73, A.74, A.105, D.106, R.111 Chain I: W.188 Chain L: T.15, G.16, A.17, S.18, S.42, A.44, T.48, S.93, I.94, K.95, T.96, R.128, E.129 25 PLIP interactions: 19 interactions with chain L, 1 interactions with chain I, 5 interactions with chain B Hydrogen bonds: L:G.16, L:G.16, L:S.18, L:S.42, L:A.45, L:S.93, L:S.93, L:I.94, L:T.96, L:R.128, L:R.128, L:E.129, B:D.106 Water bridges: L:R.43, L:A.44, L:E.70, L:K.95, L:T.96, L:N.107, B:R.111, B:R.111, B:R.111 Salt bridges: L:K.95 Hydrophobic interactions: I:W.188, B:A.74

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

PO4.2: 7 residues within 4Å: Chain A: R.128, E.129 Chain D: Y.158 Chain E: S.79, G.80, R.111, K.118 10 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D, 5 interactions with chain E Hydrogen bonds: A:E.129, D:Y.158, E:G.80 Salt bridges: A:R.128, E:R.111, E:K.118 Water bridges: D:S.156, D:R.174, E:R.111, E:K.118 PO4.4: 7 residues within 4Å: Chain B: R.128, E.129 Chain C: Y.158 Chain G: S.79, G.80, R.111, K.118 10 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C, 5 interactions with chain G Hydrogen bonds: B:E.129, C:Y.158, G:G.80 Salt bridges: B:R.128, G:R.111, G:K.118 Water bridges: C:S.156, C:R.174, G:R.111, G:K.118 PO4.6: 7 residues within 4Å: Chain B: Y.158 Chain C: R.128, E.129 Chain H: S.79, G.80, R.111, K.118 9 PLIP interactions: 2 interactions with chain B, 5 interactions with chain H, 2 interactions with chain C Water bridges: B:S.156, B:R.174, H:R.111, H:K.118 Hydrogen bonds: H:G.80, C:E.129 Salt bridges: H:R.111, H:K.118, C:R.128 PO4.8: 7 residues within 4Å: Chain A: Y.158 Chain D: R.128, E.129 Chain F: S.79, G.80, R.111, K.118 9 PLIP interactions: 5 interactions with chain F, 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: F:G.80, D:E.129 Water bridges: F:R.111, F:K.118, A:S.156, A:R.174 Salt bridges: F:R.111, F:K.118, D:R.128 PO4.10: 7 residues within 4Å: Chain E: R.128, E.129 Chain H: Y.158 Chain I: S.79, G.80, R.111, K.118 9 PLIP interactions: 5 interactions with chain I, 2 interactions with chain H, 2 interactions with chain E Hydrogen bonds: I:G.80, E:E.129 Water bridges: I:R.111, I:K.118, H:S.156, H:R.174 Salt bridges: I:R.111, I:K.118, E:R.128 PO4.12: 7 residues within 4Å: Chain F: R.128, E.129 Chain G: Y.158 Chain K: S.79, G.80, R.111, K.118 10 PLIP interactions: 2 interactions with chain F, 3 interactions with chain G, 5 interactions with chain K Hydrogen bonds: F:E.129, G:Y.158, K:G.80 Salt bridges: F:R.128, K:R.111, K:K.118 Water bridges: G:S.156, G:R.174, K:R.111, K:K.118 PO4.14: 7 residues within 4Å: Chain F: Y.158 Chain G: R.128, E.129 Chain L: S.79, G.80, R.111, K.118 9 PLIP interactions: 2 interactions with chain F, 5 interactions with chain L, 2 interactions with chain G Water bridges: F:S.156, F:R.174, L:R.111, L:K.118 Hydrogen bonds: L:G.80, G:E.129 Salt bridges: L:R.111, L:K.118, G:R.128 PO4.16: 7 residues within 4Å: Chain E: Y.158 Chain H: R.128, E.129 Chain J: S.79, G.80, R.111, K.118 10 PLIP interactions: 5 interactions with chain J, 3 interactions with chain E, 2 interactions with chain H Hydrogen bonds: J:G.80, E:Y.158, H:E.129 Water bridges: J:R.111, J:K.118, E:S.156, E:R.174 Salt bridges: J:R.111, J:K.118, H:R.128 PO4.18: 7 residues within 4Å: Chain A: S.79, G.80, R.111, K.118 Chain I: R.128, E.129 Chain L: Y.158 9 PLIP interactions: 5 interactions with chain A, 2 interactions with chain I, 2 interactions with chain L Hydrogen bonds: A:G.80, I:E.129 Water bridges: A:R.111, A:K.118, L:S.156, L:R.174 Salt bridges: A:R.111, A:K.118, I:R.128 PO4.20: 7 residues within 4Å: Chain C: S.79, G.80, R.111, K.118 Chain J: R.128, E.129 Chain K: Y.158 10 PLIP interactions: 2 interactions with chain J, 3 interactions with chain K, 5 interactions with chain C Hydrogen bonds: J:E.129, K:Y.158, C:G.80 Salt bridges: J:R.128, C:R.111, C:K.118 Water bridges: K:S.156, K:R.174, C:R.111, C:K.118 PO4.22: 7 residues within 4Å: Chain D: S.79, G.80, R.111, K.118 Chain J: Y.158 Chain K: R.128, E.129 10 PLIP interactions: 3 interactions with chain J, 2 interactions with chain K, 5 interactions with chain D Hydrogen bonds: J:Y.158, K:E.129, D:G.80 Water bridges: J:S.156, J:R.174, D:R.111, D:K.118 Salt bridges: K:R.128, D:R.111, D:K.118 PO4.24: 7 residues within 4Å: Chain B: S.79, G.80, R.111, K.118 Chain I: Y.158 Chain L: R.128, E.129 9 PLIP interactions: 2 interactions with chain I, 5 interactions with chain B, 2 interactions with chain L Water bridges: I:S.156, I:R.174, B:R.111, B:K.118 Hydrogen bonds: B:G.80, L:E.129 Salt bridges: B:R.111, B:K.118, L:R.128

Links

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Citation

Stogios, P.J., Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex. To Be Published

Release Date

2020-02-26

Peptides

Flavin prenyltransferase UbiX: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

Flavin prenyltransferase UbiX

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