SMTL ID : 6qlj.1

Crystal structure of F181Q UbiX in complex with an oxidised N5-C1' adduct derived from DMAP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-12-mer

Ligands

12 x 4LS: 1-deoxy-1-[7,8-dimethyl-5-(3-methylbut-2-en-1-yl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono -D-ribitol(Non-covalent)

4LS.1: 23 residues within 4Å: Chain A: 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 Chain C: Y.190, W.221 Chain L: W.105, M.106, A.110, S.111, C.137, R.143 Ligands: PO4.3 24 PLIP interactions: 19 interactions with chain A, 3 interactions with chain L, 2 interactions with chain C Hydrophobic interactions: A:L.65, A:V.66, L:W.105, C:Y.190, C:W.221 Hydrogen bonds: A:G.34, A:S.36, A:S.60, A:S.60, A:S.125, A:T.126, A:T.128, A:T.128, A:R.160, A:R.160, L:C.137, L:R.143 Water bridges: A:A.62, A:A.62, A:G.127, A:E.142, A:E.142, A:E.142, A:R.160 4LS.4: 23 residues within 4Å: Chain B: 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 Chain D: Y.190, W.221 Chain I: W.105, M.106, A.110, S.111, C.137, R.143 Ligands: PO4.6 24 PLIP interactions: 19 interactions with chain B, 2 interactions with chain D, 3 interactions with chain I Hydrophobic interactions: B:L.65, B:V.66, D:Y.190, D:W.221, I:W.105 Hydrogen bonds: B:G.34, B:S.36, B:S.60, B:S.60, B:S.125, B:T.126, B:T.128, B:T.128, B:R.160, B:R.160, I:C.137, I:R.143 Water bridges: B:A.62, B:A.62, B:G.127, B:E.142, B:E.142, B:E.142, B:R.160 4LS.7: 23 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, T.69, S.125, T.126, T.128, R.160, E.161 Chain K: W.105, M.106, A.110, S.111, C.137, R.143 Ligands: PO4.9 23 PLIP interactions: 18 interactions with chain C, 3 interactions with chain K, 2 interactions with chain A Hydrophobic interactions: C:L.65, C:V.66, K:W.105, A:Y.190, A:W.221 Hydrogen bonds: 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:T.128, C:R.160, C:R.160, C:E.161, K:C.137, K:R.143 Water bridges: C:A.62, C:A.62, C:G.127, C:R.160 4LS.10: 23 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, T.69, S.125, T.126, T.128, R.160, E.161 Chain J: W.105, M.106, A.110, S.111, C.137, R.143 Ligands: PO4.12 23 PLIP interactions: 18 interactions with chain D, 2 interactions with chain B, 3 interactions with chain J Hydrophobic interactions: D:L.65, D:V.66, B:Y.190, B:W.221, J:W.105 Hydrogen bonds: D:G.34, D:S.36, D:S.60, D:S.60, D:S.125, D:T.126, D:T.128, D:T.128, D:T.128, D:R.160, D:R.160, D:E.161, J:C.137, J:R.143 Water bridges: D:A.62, D:A.62, D:G.127, D:R.160 4LS.13: 23 residues within 4Å: Chain D: W.105, M.106, A.110, S.111, C.137, R.143 Chain E: 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 Chain G: Y.190, W.221 Ligands: PO4.15 25 PLIP interactions: 20 interactions with chain E, 2 interactions with chain G, 3 interactions with chain D Hydrophobic interactions: E:L.65, E:V.66, G:Y.190, G:W.221, D:W.105 Hydrogen bonds: E:G.34, E:S.36, E:S.60, E:S.60, E:S.125, E:T.126, E:T.128, E:T.128, E:T.128, E:R.160, E:R.160, D:C.137, D:R.143 Water bridges: E:A.62, E:A.62, E:G.127, E:E.142, E:E.142, E:E.142, E:R.160 4LS.16: 23 residues within 4Å: Chain A: W.105, M.106, A.110, S.111, C.137, R.143 Chain F: 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 Chain H: Y.190, W.221 Ligands: PO4.18 22 PLIP interactions: 17 interactions with chain F, 3 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: F:L.65, F:V.66, A:W.105, H:Y.190, H:W.221 Hydrogen bonds: F:G.34, F:S.36, F:S.60, F:S.60, F:S.125, F:T.126, F:T.128, F:T.128, F:R.160, F:R.160, F:E.161, A:C.137, A:R.143 Water bridges: F:A.62, F:A.62, F:G.127, F:R.160 4LS.19: 23 residues within 4Å: Chain C: W.105, M.106, A.110, S.111, 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, T.69, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.21 25 PLIP interactions: 20 interactions with chain G, 2 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: G:L.65, G:V.66, E:Y.190, E:W.221, C:W.105 Hydrogen bonds: G:G.34, G:S.36, G:S.60, G:S.60, G:S.125, G:T.126, G:T.128, G:T.128, G:T.128, G:R.160, G:R.160, C:C.137, C:R.143 Water bridges: G:A.62, G:A.62, G:G.127, G:E.142, G:E.142, G:E.142, G:R.160 4LS.22: 23 residues within 4Å: Chain B: W.105, M.106, A.110, S.111, 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, T.69, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.24 22 PLIP interactions: 3 interactions with chain B, 17 interactions with chain H, 2 interactions with chain F Hydrophobic interactions: B:W.105, H:L.65, H:V.66, F:Y.190, F:W.221 Hydrogen bonds: B:C.137, B:R.143, H:G.34, H:S.36, H:S.60, H:S.60, H:S.125, H:T.126, H:T.128, H:T.128, H:R.160, H:R.160, H:E.161 Water bridges: H:A.62, H:A.62, H:G.127, H:R.160 4LS.25: 23 residues within 4Å: Chain H: W.105, M.106, 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 Chain K: Y.190, W.221 Ligands: PO4.27 22 PLIP interactions: 3 interactions with chain H, 17 interactions with chain I, 2 interactions with chain K Hydrophobic interactions: H:W.105, I:L.65, I:V.66, K:Y.190, K:W.221 Hydrogen bonds: H:C.137, H:R.143, 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:T.128, I:R.160, I:R.160 Water bridges: I:A.62, I:A.62, I:G.127, I:R.160 4LS.28: 23 residues within 4Å: Chain E: W.105, M.106, A.110, S.111, C.137, R.143 Chain J: 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 Chain L: Y.190, W.221 Ligands: PO4.30 25 PLIP interactions: 20 interactions with chain J, 2 interactions with chain L, 3 interactions with chain E Hydrophobic interactions: J:L.65, J:V.66, L:Y.190, L:W.221, E:W.105 Hydrogen bonds: J:G.34, J:S.36, J:S.60, J:S.60, J:S.125, J:T.126, J:T.128, J:T.128, J:R.160, J:R.160, J:E.161, E:C.137, E:R.143 Water bridges: J:A.62, J:A.62, J:G.127, J:E.142, J:E.142, J:E.142, J:R.160 4LS.31: 23 residues within 4Å: Chain G: W.105, M.106, A.110, S.111, 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, T.69, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.33 25 PLIP interactions: 3 interactions with chain G, 20 interactions with chain K, 2 interactions with chain I Hydrophobic interactions: G:W.105, K:L.65, K:V.66, I:Y.190, I:W.221 Hydrogen bonds: G:C.137, G:R.143, 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:E.142, K:E.142, K:E.142, K:R.160 4LS.34: 23 residues within 4Å: Chain F: W.105, M.106, A.110, S.111, 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, T.69, S.125, T.126, T.128, R.160, E.161 Ligands: PO4.36 22 PLIP interactions: 17 interactions with chain L, 3 interactions with chain F, 2 interactions with chain J Hydrophobic interactions: L:L.65, L:V.66, F:W.105, J:Y.190, J:W.221 Hydrogen bonds: L:G.34, L:S.36, L:S.60, L:S.60, L:S.125, L:T.126, L:T.128, L:T.128, L:T.128, L:R.160, L:R.160, F:C.137, F:R.143 Water bridges: L:A.62, L:A.62, L:G.127, L:R.160

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

NA.2: 3 residues within 4Å: Chain A: A.136, N.138 Chain F: E.142 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:E.142 Water bridges: A:N.138, A:N.138 NA.5: 3 residues within 4Å: Chain B: A.136, N.138 Chain H: E.142 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain H Water bridges: B:N.138, B:N.138 Hydrogen bonds: H:E.142 NA.8: 3 residues within 4Å: Chain C: A.136, N.138 Chain G: E.142 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain C Hydrogen bonds: G:E.142 Water bridges: C:N.138, C:N.138 NA.11: 3 residues within 4Å: Chain D: A.136, N.138 Chain E: E.142 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.136 Water bridges: D:N.138, D:N.138 NA.14: 3 residues within 4Å: Chain E: A.136, N.138 Chain J: E.142 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.136 Water bridges: E:N.138, E:N.138 NA.17: 3 residues within 4Å: Chain F: A.136, N.138 Chain L: E.142 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain F Hydrogen bonds: L:E.142 Water bridges: F:N.138, F:N.138 NA.20: 3 residues within 4Å: Chain G: A.136, N.138 Chain K: E.142 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:A.136 Water bridges: G:N.138, G:N.138 NA.23: 3 residues within 4Å: Chain H: A.136, N.138 Chain I: E.142 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:A.136 Water bridges: H:N.138, H:N.138 NA.26: 3 residues within 4Å: Chain B: E.142 Chain I: A.136, N.138 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:A.136 Water bridges: I:N.138, I:N.138 NA.29: 3 residues within 4Å: Chain D: E.142 Chain J: A.136, N.138 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain J Hydrogen bonds: D:E.142 Water bridges: J:N.138, J:N.138 NA.32: 3 residues within 4Å: Chain C: E.142 Chain K: A.136, N.138 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain K Hydrogen bonds: C:E.142 Water bridges: K:N.138, K:N.138 NA.35: 3 residues within 4Å: Chain A: E.142 Chain L: A.136, N.138 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain A Water bridges: L:N.138, L:N.138 Hydrogen bonds: A:E.142

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

PO4.3: 9 residues within 4Å: Chain A: R.160, E.161 Chain C: Y.190, R.206 Chain L: S.111, G.112, R.143, K.150 Ligands: 4LS.1 8 PLIP interactions: 4 interactions with chain L, 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: L:G.112, L:S.113, C:Y.190, C:Y.190 Salt bridges: L:R.143, L:K.150, C:R.206, A:R.160 PO4.6: 9 residues within 4Å: Chain B: R.160, E.161 Chain D: Y.190, R.206 Chain I: S.111, G.112, R.143, K.150 Ligands: 4LS.4 8 PLIP interactions: 4 interactions with chain I, 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: I:G.112, I:S.113, D:Y.190, D:Y.190 Salt bridges: I:R.143, I:K.150, B:R.160, D:R.206 PO4.9: 9 residues within 4Å: Chain A: Y.190, R.206 Chain C: R.160, E.161 Chain K: S.111, G.112, R.143, K.150 Ligands: 4LS.7 7 PLIP interactions: 4 interactions with chain K, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: K:G.112, K:S.113, A:Y.190 Salt bridges: K:R.143, K:K.150, C:R.160, A:R.206 PO4.12: 9 residues within 4Å: Chain B: Y.190, R.206 Chain D: R.160, E.161 Chain J: S.111, G.112, R.143, K.150 Ligands: 4LS.10 7 PLIP interactions: 2 interactions with chain B, 4 interactions with chain J, 1 interactions with chain D Hydrogen bonds: B:Y.190, J:G.112, J:S.113 Salt bridges: B:R.206, J:R.143, J:K.150, D:R.160 PO4.15: 9 residues within 4Å: Chain D: S.111, G.112, R.143, K.150 Chain E: R.160, E.161 Chain G: Y.190, R.206 Ligands: 4LS.13 8 PLIP interactions: 1 interactions with chain E, 4 interactions with chain D, 3 interactions with chain G Salt bridges: E:R.160, D:R.143, D:K.150, G:R.206 Hydrogen bonds: D:G.112, D:S.113, G:Y.190, G:Y.190 PO4.18: 9 residues within 4Å: Chain A: S.111, G.112, R.143, K.150 Chain F: R.160, E.161 Chain H: Y.190, R.206 Ligands: 4LS.16 7 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F, 2 interactions with chain H Hydrogen bonds: A:G.112, A:S.113, H:Y.190 Salt bridges: A:R.143, A:K.150, F:R.160, H:R.206 PO4.21: 9 residues within 4Å: Chain C: S.111, G.112, R.143, K.150 Chain E: Y.190, R.206 Chain G: R.160, E.161 Ligands: 4LS.19 8 PLIP interactions: 3 interactions with chain E, 4 interactions with chain C, 1 interactions with chain G Hydrogen bonds: E:Y.190, E:Y.190, C:G.112, C:S.113 Salt bridges: E:R.206, C:R.143, C:K.150, G:R.160 PO4.24: 9 residues within 4Å: Chain B: S.111, G.112, R.143, K.150 Chain F: Y.190, R.206 Chain H: R.160, E.161 Ligands: 4LS.22 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain H, 2 interactions with chain F Hydrogen bonds: B:G.112, B:S.113, F:Y.190 Salt bridges: B:R.143, B:K.150, H:R.160, F:R.206 PO4.27: 9 residues within 4Å: Chain H: S.111, G.112, R.143, K.150 Chain I: R.160, E.161 Chain K: Y.190, R.206 Ligands: 4LS.25 7 PLIP interactions: 2 interactions with chain K, 4 interactions with chain H, 1 interactions with chain I Hydrogen bonds: K:Y.190, H:G.112, H:S.113 Salt bridges: K:R.206, H:R.143, H:K.150, I:R.160 PO4.30: 9 residues within 4Å: Chain E: S.111, G.112, R.143, K.150 Chain J: R.160, E.161 Chain L: Y.190, R.206 Ligands: 4LS.28 8 PLIP interactions: 4 interactions with chain E, 3 interactions with chain L, 1 interactions with chain J Hydrogen bonds: E:G.112, E:S.113, L:Y.190, L:Y.190 Salt bridges: E:R.143, E:K.150, L:R.206, J:R.160 PO4.33: 9 residues within 4Å: Chain G: S.111, G.112, R.143, K.150 Chain I: Y.190, R.206 Chain K: R.160, E.161 Ligands: 4LS.31 8 PLIP interactions: 4 interactions with chain G, 3 interactions with chain I, 1 interactions with chain K Hydrogen bonds: G:G.112, G:S.113, I:Y.190, I:Y.190 Salt bridges: G:R.143, G:K.150, I:R.206, K:R.160 PO4.36: 9 residues within 4Å: Chain F: S.111, G.112, R.143, K.150 Chain J: Y.190, R.206 Chain L: R.160, E.161 Ligands: 4LS.34 7 PLIP interactions: 4 interactions with chain F, 2 interactions with chain J, 1 interactions with chain L Hydrogen bonds: F:G.112, F:S.113, J:Y.190 Salt bridges: F:R.143, F:K.150, J:R.206, L: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
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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