SMTL ID : 6qlk.1

Crystal structure of F181H UbiX in complex with prFMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-12-mer

Ligands

12 x 4LU: 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol(Non-covalent)

4LU.1: 20 residues within 4Å: Chain A: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain C: Y.190, W.221 Chain L: W.105, C.137, R.143 Ligands: PO4.2 24 PLIP interactions: 20 interactions with chain A, 3 interactions with chain C, 1 interactions with chain L Hydrophobic interactions: A:L.65, A:V.66, C:Y.190, C:Y.190, C:W.221, L:W.105 Hydrogen bonds: A:G.34, A:G.34, A:S.36, A:S.60, A:S.60, A:S.125, A:S.125, A:T.126, A:T.128, A:R.160, A:R.160 Water bridges: A:K.61, A:A.62, A:G.127, A:E.142, A:E.142, A:E.142, A:R.160 4LU.4: 20 residues within 4Å: Chain B: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain D: Y.190, W.221 Chain I: W.105, C.137, R.143 Ligands: PO4.5 24 PLIP interactions: 3 interactions with chain D, 20 interactions with chain B, 1 interactions with chain I Hydrophobic interactions: D:Y.190, D:Y.190, D:W.221, 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.60, B:S.125, B:S.125, B:T.126, B:T.128, B:R.160, B:R.160 Water bridges: B:K.61, B:A.62, B:G.127, B:E.142, B:E.142, B:E.142, B:R.160 4LU.7: 20 residues within 4Å: Chain A: Y.190, W.221 Chain C: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain K: W.105, C.137, R.143 Ligands: PO4.8 23 PLIP interactions: 19 interactions with chain C, 3 interactions with chain A, 1 interactions with chain K Hydrophobic interactions: C:L.65, C:V.66, A:Y.190, A:Y.190, A:W.221, K:W.105 Hydrogen bonds: C:G.34, C:G.34, C:S.36, C:S.60, C:S.60, C:S.125, C:S.125, C:T.126, C:T.128, C:T.128, C:R.160, C:R.160, C:E.161 Water bridges: C:K.61, C:A.62, C:G.127, C:R.160 4LU.10: 20 residues within 4Å: Chain B: Y.190, W.221 Chain D: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain J: W.105, C.137, R.143 Ligands: PO4.11 23 PLIP interactions: 19 interactions with chain D, 1 interactions with chain J, 3 interactions with chain B Hydrophobic interactions: D:L.65, D:V.66, J:W.105, B:Y.190, B:Y.190, B:W.221 Hydrogen bonds: D:G.34, D:G.34, D:S.36, D:S.60, 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 Water bridges: D:K.61, D:A.62, D:G.127, D:R.160 4LU.13: 20 residues within 4Å: Chain D: W.105, C.137, R.143 Chain E: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain G: Y.190, W.221 Ligands: PO4.14 25 PLIP interactions: 21 interactions with chain E, 3 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: E:L.65, E:V.66, G:Y.190, G:Y.190, G:W.221, D:W.105 Hydrogen bonds: E:G.34, E:G.34, E:S.36, E:S.60, E:S.60, E:S.125, E:S.125, E:T.126, E:T.128, E:T.128, E:R.160, E:R.160 Water bridges: E:K.61, E:A.62, E:G.127, E:E.142, E:E.142, E:E.142, E:R.160 4LU.16: 20 residues within 4Å: Chain A: W.105, C.137, R.143 Chain F: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain H: Y.190, W.221 Ligands: PO4.17 22 PLIP interactions: 18 interactions with chain F, 1 interactions with chain A, 3 interactions with chain H Hydrophobic interactions: F:L.65, F:V.66, A:W.105, H:Y.190, H:Y.190, H:W.221 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:R.160, F:R.160, F:E.161 Water bridges: F:K.61, F:A.62, F:G.127, F:R.160 4LU.19: 20 residues within 4Å: Chain C: W.105, C.137, R.143 Chain E: Y.190, W.221 Chain G: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.20 25 PLIP interactions: 21 interactions with chain G, 3 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: G:L.65, G:V.66, E:Y.190, E:Y.190, E:W.221, C:W.105 Hydrogen bonds: G:G.34, G:G.34, G:S.36, G:S.60, G:S.60, G:S.125, G:S.125, G:T.126, G:T.128, G:T.128, G:R.160, G:R.160 Water bridges: G:K.61, G:A.62, G:G.127, G:E.142, G:E.142, G:E.142, G:R.160 4LU.22: 20 residues within 4Å: Chain B: W.105, C.137, R.143 Chain F: Y.190, W.221 Chain H: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.23 22 PLIP interactions: 1 interactions with chain B, 18 interactions with chain H, 3 interactions with chain F Hydrophobic interactions: B:W.105, H:L.65, H:V.66, F:Y.190, F:Y.190, F:W.221 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 Water bridges: H:K.61, H:A.62, H:G.127, H:R.160 4LU.25: 20 residues within 4Å: Chain H: W.105, C.137, R.143 Chain I: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain K: Y.190, W.221 Ligands: PO4.26 22 PLIP interactions: 18 interactions with chain I, 3 interactions with chain K, 1 interactions with chain H Hydrophobic interactions: I:L.65, I:V.66, K:Y.190, K:Y.190, K:W.221, H:W.105 Hydrogen bonds: I:G.34, I:G.34, I:S.36, I:S.60, I:S.60, I:S.125, I:S.125, I:T.126, I:T.128, I:T.128, I:R.160, I:R.160 Water bridges: I:K.61, I:A.62, I:G.127, I:R.160 4LU.28: 20 residues within 4Å: Chain E: W.105, C.137, R.143 Chain J: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Chain L: Y.190, W.221 Ligands: PO4.29 25 PLIP interactions: 1 interactions with chain E, 3 interactions with chain L, 21 interactions with chain J Hydrophobic interactions: E:W.105, L:Y.190, L:Y.190, L:W.221, J:L.65, J:V.66 Hydrogen bonds: 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, J:E.161 Water bridges: J:K.61, J:A.62, J:G.127, J:E.142, J:E.142, J:E.142, J:R.160 4LU.31: 20 residues within 4Å: Chain G: W.105, C.137, R.143 Chain I: Y.190, W.221 Chain K: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.32 25 PLIP interactions: 21 interactions with chain K, 3 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: K:L.65, K:V.66, I:Y.190, I:Y.190, I:W.221, G:W.105 Hydrogen bonds: K:G.34, K:G.34, K:S.36, K:S.60, K:S.60, K:S.125, K:S.125, K:T.126, K:T.128, K:R.160, K:R.160, K:E.161 Water bridges: K:K.61, K:A.62, K:G.127, K:E.142, K:E.142, K:E.142, K:R.160 4LU.34: 20 residues within 4Å: Chain F: W.105, C.137, R.143 Chain J: Y.190, W.221 Chain L: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, E.70, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.35 22 PLIP interactions: 18 interactions with chain L, 3 interactions with chain J, 1 interactions with chain F Hydrophobic interactions: L:L.65, L:V.66, J:Y.190, J:Y.190, J:W.221, F:W.105 Hydrogen bonds: L:G.34, L:G.34, L:S.36, L:S.60, L:S.60, L:S.125, L:S.125, L:T.126, L:T.128, L:T.128, L:R.160, L:R.160 Water bridges: L:K.61, L:A.62, L:G.127, L:R.160

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

PO4.2: 10 residues within 4Å: Chain A: R.160, E.161 Chain C: Y.190, R.206 Chain L: S.111, G.112, S.113, R.143, K.150 Ligands: 4LU.1 9 PLIP interactions: 6 interactions with chain L, 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: L:G.112, L:S.113, C:Y.190 Water bridges: L:R.143, L:R.143 Salt bridges: L:R.143, L:K.150, A:R.160, C:R.206 PO4.5: 10 residues within 4Å: Chain B: R.160, E.161 Chain D: Y.190, R.206 Chain I: S.111, G.112, S.113, R.143, K.150 Ligands: 4LU.4 9 PLIP interactions: 6 interactions with chain I, 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: I:G.112, I:S.113, D:Y.190 Water bridges: I:R.143, I:R.143 Salt bridges: I:R.143, I:K.150, D:R.206, B:R.160 PO4.8: 10 residues within 4Å: Chain A: Y.190, R.206 Chain C: R.160, E.161 Chain K: S.111, G.112, S.113, R.143, K.150 Ligands: 4LU.7 8 PLIP interactions: 6 interactions with chain K, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: K:G.112, K:S.113 Water bridges: K:R.143, K:R.143 Salt bridges: K:R.143, K:K.150, A:R.206, C:R.160 PO4.11: 10 residues within 4Å: Chain B: Y.190, R.206 Chain D: R.160, E.161 Chain J: S.111, G.112, S.113, R.143, K.150 Ligands: 4LU.10 8 PLIP interactions: 1 interactions with chain B, 6 interactions with chain J, 1 interactions with chain D Salt bridges: B:R.206, J:R.143, J:K.150, D:R.160 Hydrogen bonds: J:G.112, J:S.113 Water bridges: J:R.143, J:R.143 PO4.14: 10 residues within 4Å: Chain D: S.111, G.112, S.113, R.143, K.150 Chain E: R.160, E.161 Chain G: Y.190, R.206 Ligands: 4LU.13 9 PLIP interactions: 2 interactions with chain G, 6 interactions with chain D, 1 interactions with chain E Hydrogen bonds: G:Y.190, D:G.112, D:S.113 Salt bridges: G:R.206, D:R.143, D:K.150, E:R.160 Water bridges: D:R.143, D:R.143 PO4.17: 10 residues within 4Å: Chain A: S.111, G.112, S.113, R.143, K.150 Chain F: R.160, E.161 Chain H: Y.190, R.206 Ligands: 4LU.16 8 PLIP interactions: 6 interactions with chain A, 1 interactions with chain F, 1 interactions with chain H Hydrogen bonds: A:G.112, A:S.113 Water bridges: A:R.143, A:R.143 Salt bridges: A:R.143, A:K.150, F:R.160, H:R.206 PO4.20: 10 residues within 4Å: Chain C: S.111, G.112, S.113, R.143, K.150 Chain E: Y.190, R.206 Chain G: R.160, E.161 Ligands: 4LU.19 9 PLIP interactions: 6 interactions with chain C, 2 interactions with chain E, 1 interactions with chain G Hydrogen bonds: C:G.112, C:S.113, E:Y.190 Water bridges: C:R.143, C:R.143 Salt bridges: C:R.143, C:K.150, E:R.206, G:R.160 PO4.23: 10 residues within 4Å: Chain B: S.111, G.112, S.113, R.143, K.150 Chain F: Y.190, R.206 Chain H: R.160, E.161 Ligands: 4LU.22 8 PLIP interactions: 1 interactions with chain F, 6 interactions with chain B, 1 interactions with chain H Salt bridges: F:R.206, B:R.143, B:K.150, H:R.160 Hydrogen bonds: B:G.112, B:S.113 Water bridges: B:R.143, B:R.143 PO4.26: 10 residues within 4Å: Chain H: S.111, G.112, S.113, R.143, K.150 Chain I: R.160, E.161 Chain K: Y.190, R.206 Ligands: 4LU.25 8 PLIP interactions: 6 interactions with chain H, 1 interactions with chain K, 1 interactions with chain I Hydrogen bonds: H:G.112, H:S.113 Water bridges: H:R.143, H:R.143 Salt bridges: H:R.143, H:K.150, K:R.206, I:R.160 PO4.29: 10 residues within 4Å: Chain E: S.111, G.112, S.113, R.143, K.150 Chain J: R.160, E.161 Chain L: Y.190, R.206 Ligands: 4LU.28 9 PLIP interactions: 2 interactions with chain L, 6 interactions with chain E, 1 interactions with chain J Hydrogen bonds: L:Y.190, E:G.112, E:S.113 Salt bridges: L:R.206, E:R.143, E:K.150, J:R.160 Water bridges: E:R.143, E:R.143 PO4.32: 10 residues within 4Å: Chain G: S.111, G.112, S.113, R.143, K.150 Chain I: Y.190, R.206 Chain K: R.160, E.161 Ligands: 4LU.31 9 PLIP interactions: 6 interactions with chain G, 2 interactions with chain I, 1 interactions with chain K Hydrogen bonds: G:G.112, G:S.113, I:Y.190 Water bridges: G:R.143, G:R.143 Salt bridges: G:R.143, G:K.150, I:R.206, K:R.160 PO4.35: 10 residues within 4Å: Chain F: S.111, G.112, S.113, R.143, K.150 Chain J: Y.190, R.206 Chain L: R.160, E.161 Ligands: 4LU.34 8 PLIP interactions: 6 interactions with chain F, 1 interactions with chain L, 1 interactions with chain J Hydrogen bonds: F:G.112, F:S.113 Water bridges: F:R.143, F:R.143 Salt bridges: F:R.143, F:K.150, L:R.160, J:R.206

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

NA.3: 3 residues within 4Å: Chain A: A.136, N.138 Chain F: E.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.136 NA.6: 3 residues within 4Å: Chain B: A.136, N.138 Chain H: E.142 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:E.142 NA.9: 3 residues within 4Å: Chain C: A.136, N.138 Chain G: E.142 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.136 NA.12: 3 residues within 4Å: Chain D: A.136, N.138 Chain E: E.142 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.136 NA.15: 3 residues within 4Å: Chain E: A.136, N.138 Chain J: E.142 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.142 NA.18: 3 residues within 4Å: Chain F: A.136, N.138 Chain L: E.142 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.136 NA.21: 3 residues within 4Å: Chain G: A.136, N.138 Chain K: E.142 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.142 NA.24: 3 residues within 4Å: Chain H: A.136, N.138 Chain I: E.142 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.142 NA.27: 3 residues within 4Å: Chain B: E.142 Chain I: A.136, N.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.142 NA.30: 3 residues within 4Å: Chain D: E.142 Chain J: A.136, N.138 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:A.136 NA.33: 3 residues within 4Å: Chain C: E.142 Chain K: A.136, N.138 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:A.136 NA.36: 3 residues within 4Å: Chain A: E.142 Chain L: A.136, N.138 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:A.136

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
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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