SMTL ID : 5m1e.1

Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-hexamer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: N.195, E.261 Ligands: 7D9.2, NA.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.261, A:E.261, H2O.1, H2O.1 MN.4: 4 residues within 4Å: Chain B: N.195, E.261 Ligands: 7D9.5, NA.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.261, B:E.261, H2O.2, H2O.2 MN.7: 4 residues within 4Å: Chain C: N.195, E.261 Ligands: 7D9.8, NA.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.261, C:E.261 MN.10: 4 residues within 4Å: Chain D: N.195, E.261 Ligands: 7D9.11, NA.12 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.261, D:E.261, H2O.6, H2O.6 MN.13: 4 residues within 4Å: Chain E: N.195, E.261 Ligands: 7D9.14, NA.15 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.261, E:E.261, H2O.7, H2O.7 MN.16: 4 residues within 4Å: Chain F: N.195, E.261 Ligands: 7D9.17, NA.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.261, F:E.261

6 x 7D9: (16~{R})-11,12,14,14-tetramethyl-3,5-bis(oxidanylidene)-8-[(2~{S},3~{S},4~{R})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),9(17),10,12-tetraene-16-sulfonic acid(Non-covalent)

7D9.2: 20 residues within 4Å: Chain A: T.180, N.195, L.196, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, T.340, T.342, P.349 Ligands: MN.1, NA.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.180, A:I.198, A:I.198, A:R.200, A:V.252, A:T.340, A:T.342, A:P.349 Hydrogen bonds: A:I.198, A:I.198, A:Y.199, A:R.200, A:R.212, A:R.212, A:L.214, A:R.217, A:R.217, A:G.218, A:V.252, A:H.311, A:T.342 Water bridges: A:E.261 7D9.5: 22 residues within 4Å: Chain B: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, H.311, T.340, T.342, P.349 Ligands: MN.4, NA.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:T.180, B:W.181, B:I.198, B:I.198, B:R.200, B:V.252, B:T.340, B:P.349 Hydrogen bonds: B:N.195, B:I.198, B:I.198, B:Y.199, B:R.200, B:R.200, B:R.212, B:R.212, B:L.214, B:R.217, B:R.217, B:G.218, B:V.252, B:D.310, B:H.311, B:T.342 Water bridges: B:R.212, B:R.212, B:E.261 Salt bridges: B:R.212 7D9.8: 23 residues within 4Å: Chain C: T.180, W.181, N.195, L.196, G.197, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, H.311, T.340, T.342, P.349 Ligands: MN.7, NA.9 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:W.181, C:I.198, C:I.198, C:R.200, C:V.252, C:P.349 Hydrogen bonds: C:N.195, C:I.198, C:I.198, C:Y.199, C:R.200, C:R.200, C:R.212, C:R.212, C:L.214, C:R.217, C:R.217, C:G.218, C:V.252, C:E.261, C:E.261, C:D.310, C:H.311 Salt bridges: C:R.212 7D9.11: 20 residues within 4Å: Chain D: T.180, N.195, L.196, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, T.340, T.342, P.349 Ligands: MN.10, NA.12 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.180, D:I.198, D:I.198, D:R.200, D:V.252, D:T.340, D:T.342, D:P.349 Hydrogen bonds: D:I.198, D:I.198, D:R.200, D:R.212, D:R.212, D:L.214, D:R.217, D:R.217, D:G.218, D:V.252, D:H.311 Water bridges: D:E.261 7D9.14: 22 residues within 4Å: Chain E: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, H.311, T.340, T.342, P.349 Ligands: MN.13, NA.15 25 PLIP interactions: 25 interactions with chain E Hydrophobic interactions: E:T.180, E:W.181, E:I.198, E:I.198, E:R.200, E:V.252, E:T.340, E:P.349 Hydrogen bonds: E:N.195, E:I.198, E:I.198, E:R.200, E:R.200, E:R.212, E:R.212, E:L.214, E:R.217, E:R.217, E:G.218, E:V.252, E:H.311 Water bridges: E:R.212, E:R.212, E:E.261 Salt bridges: E:R.212 7D9.17: 23 residues within 4Å: Chain F: T.180, W.181, N.195, L.196, G.197, I.198, Y.199, R.200, R.212, W.213, L.214, R.217, G.218, A.251, V.252, E.261, D.310, H.311, T.340, T.342, P.349 Ligands: MN.16, NA.18 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:W.181, F:I.198, F:I.198, F:R.200, F:V.252, F:P.349 Hydrogen bonds: F:I.198, F:I.198, F:R.200, F:R.200, F:R.212, F:R.212, F:L.214, F:R.217, F:R.217, F:G.218, F:V.252, F:E.261, F:E.261, F:H.311, F:T.342 Salt bridges: F:R.212

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

NA.3: 6 residues within 4Å: Chain A: N.195, L.196, A.251, E.261 Ligands: MN.1, 7D9.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.261 NA.6: 6 residues within 4Å: Chain B: L.196, G.197, A.251, E.261 Ligands: MN.4, 7D9.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.261 NA.9: 6 residues within 4Å: Chain C: L.196, A.251, T.253, E.261 Ligands: MN.7, 7D9.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.261 NA.12: 6 residues within 4Å: Chain D: N.195, L.196, A.251, E.261 Ligands: MN.10, 7D9.11 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.196 NA.15: 6 residues within 4Å: Chain E: L.196, G.197, A.251, E.261 Ligands: MN.13, 7D9.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.261 NA.18: 6 residues within 4Å: Chain F: L.196, A.251, T.253, E.261 Ligands: MN.16, 7D9.17 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marshall, S.A. et al., Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis. J. Biol. Chem. (2017)

Release Date

2017-01-11

Peptides

3-octaprenyl-4-hydroxybenzoate carboxy-lyase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Related Entries With Identical Sequence