SMTL ID : 5m1d.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: N.195, L.196, E.261 Ligands: 4LU.2, NA.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.261, A:E.261 MN.4: 4 residues within 4Å: Chain B: N.195, E.261 Ligands: 4LU.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.3 MN.8: 4 residues within 4Å: Chain C: N.195, E.261 Ligands: 4LU.9, NA.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.261, C:E.261 MN.11: 5 residues within 4Å: Chain D: N.195, L.196, E.261 Ligands: 4LU.12, NA.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.261, D:E.261 MN.14: 4 residues within 4Å: Chain E: N.195, E.261 Ligands: 4LU.15, NA.16 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.261, E:E.261, H2O.8, H2O.8 MN.18: 4 residues within 4Å: Chain F: N.195, E.261 Ligands: 4LU.19, NA.20 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:E.261, F:E.261

6 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.2: 19 residues within 4Å: Chain A: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342, P.349 Ligands: MN.1, NA.3 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.180, A:W.181, A:I.198, A:I.198, A:R.200, 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:E.261 4LU.5: 18 residues within 4Å: Chain B: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342 Ligands: MN.4, NA.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:W.181, B:I.198, B:I.198, B:R.200, B:V.252 Hydrogen bonds: B:N.195, B:I.198, B:I.198, B:Y.199, 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:E.261 4LU.9: 21 residues within 4Å: Chain C: T.180, W.181, N.195, L.196, G.197, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342, P.349, L.352 Ligands: MN.8, NA.10 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:W.181, C:I.198, C:I.198, C:R.200, C:P.349, C:L.352 Hydrogen bonds: C:N.195, C:I.198, C:I.198, C:Y.199, 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 4LU.12: 19 residues within 4Å: Chain D: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342, P.349 Ligands: MN.11, NA.13 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.180, D:W.181, D:I.198, D:I.198, D:R.200, 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:E.261 4LU.15: 18 residues within 4Å: Chain E: T.180, W.181, N.195, L.196, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342 Ligands: MN.14, NA.16 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:W.181, E:I.198, E:I.198, E:R.200, E:V.252 Hydrogen bonds: E:N.195, E:I.198, E:I.198, 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:E.261 4LU.19: 21 residues within 4Å: Chain F: T.180, W.181, N.195, L.196, G.197, I.198, Y.199, R.200, R.212, L.214, R.217, G.218, A.251, V.252, E.261, T.340, T.342, P.349, L.352 Ligands: MN.18, NA.20 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:W.181, F:I.198, F:I.198, F:R.200, F:P.349, F:L.352 Hydrogen bonds: F:I.198, F:I.198, 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

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

NA.3: 6 residues within 4Å: Chain A: L.196, A.251, T.253, E.261 Ligands: MN.1, 4LU.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, 4LU.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.251 NA.10: 6 residues within 4Å: Chain C: L.196, A.251, T.253, E.261 Ligands: MN.8, 4LU.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.253 NA.13: 6 residues within 4Å: Chain D: L.196, A.251, T.253, E.261 Ligands: MN.11, 4LU.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.196 NA.16: 6 residues within 4Å: Chain E: L.196, G.197, A.251, E.261 Ligands: MN.14, 4LU.15 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:L.196 NA.20: 6 residues within 4Å: Chain F: L.196, A.251, T.253, E.261 Ligands: MN.18, 4LU.19 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.251

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain B: L.409, R.410, Q.411 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.410, B:Q.411, B:Q.411 Salt bridges: B:R.410 SO4.17: 3 residues within 4Å: Chain E: L.409, R.410, Q.411 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.410, E:Q.411, E:Q.411 Salt bridges: E:R.410

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