SMTL ID : 6h6v.1

Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.66 Å

Oligo State

homo-hexamer

Ligands

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 19 residues within 4Å: Chain A: N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, E.210, H.296, L.299 Ligands: K.2, MN.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.150, A:L.299 Hydrogen bonds: A:N.147, A:I.150, A:I.150, A:H.151, A:R.152, A:L.164, A:L.166, A:R.168, A:H.169, A:L.170, A:Q.201, A:Q.201 Water bridges: A:S.149, A:R.168, A:H.169, A:T.204 Salt bridges: A:H.169 pi-Cation interactions: A:H.151 FMN.5: 21 residues within 4Å: Chain B: T.132, N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, A.202, E.210, H.296, L.299 Ligands: K.6, MN.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.150, B:L.299 Hydrogen bonds: B:N.147, B:I.150, B:I.150, B:H.151, B:R.152, B:L.164, B:L.166, B:R.168, B:H.169, B:L.170, B:Q.201, B:Q.201 Water bridges: B:S.149, B:S.149, B:T.204 Salt bridges: B:H.169 pi-Cation interactions: B:H.151 FMN.9: 19 residues within 4Å: Chain C: N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, E.210, H.296, L.299 Ligands: K.10, MN.11 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.150, C:L.299 Hydrogen bonds: C:N.147, C:I.150, C:I.150, C:H.151, C:R.152, C:L.164, C:L.166, C:R.168, C:H.169, C:L.170, C:Q.201, C:Q.201 Water bridges: C:S.149, C:R.168 Salt bridges: C:H.169 pi-Cation interactions: C:H.151 FMN.13: 19 residues within 4Å: Chain D: N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, E.210, H.296, L.299 Ligands: K.14, MN.15 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.150, D:L.299 Hydrogen bonds: D:N.147, D:I.150, D:I.150, D:R.152, D:L.164, D:L.166, D:R.168, D:H.169, D:L.170, D:Q.201, D:Q.201 Water bridges: D:S.149, D:H.151, D:R.168, D:H.169 Salt bridges: D:H.169 FMN.17: 20 residues within 4Å: Chain E: N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, A.202, E.210, H.296, L.299 Ligands: K.18, MN.19 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:I.150, E:L.299 Hydrogen bonds: E:N.147, E:I.150, E:I.150, E:R.152, E:L.164, E:L.166, E:R.168, E:H.169, E:L.170, E:Q.201, E:Q.201 Water bridges: E:S.149, E:H.151, E:R.168, E:T.204 Salt bridges: E:H.169 FMN.21: 19 residues within 4Å: Chain F: N.147, V.148, S.149, I.150, H.151, R.152, L.164, I.165, L.166, R.168, H.169, L.170, S.200, Q.201, E.210, H.296, L.299 Ligands: K.22, MN.23 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:I.150, F:L.299 Hydrogen bonds: F:N.147, F:I.150, F:I.150, F:R.152, F:L.164, F:L.166, F:R.168, F:H.169, F:L.170, F:Q.201, F:Q.201 Water bridges: F:S.149, F:S.149, F:R.168 Salt bridges: F:H.169

6 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: V.148, S.200, A.202, E.210 Ligands: FMN.1, MN.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.148, A:S.200, A:E.210, H2O.1 K.6: 6 residues within 4Å: Chain B: V.148, S.200, A.202, E.210 Ligands: FMN.5, MN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.148, B:S.200, B:E.210 K.10: 6 residues within 4Å: Chain C: V.148, S.200, A.202, E.210 Ligands: FMN.9, MN.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.200, C:E.210 K.14: 6 residues within 4Å: Chain D: V.148, S.200, A.202, E.210 Ligands: FMN.13, MN.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.148, D:S.200, D:E.210 K.18: 6 residues within 4Å: Chain E: V.148, S.200, A.202, E.210 Ligands: FMN.17, MN.19 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:V.148, E:S.200, E:E.210 K.22: 6 residues within 4Å: Chain F: V.148, S.200, A.202, E.210 Ligands: FMN.21, MN.23 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:S.200, F:A.202, F:E.210

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

MN.3: 5 residues within 4Å: Chain A: N.147, H.169, E.210 Ligands: FMN.1, K.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.169, A:E.210, H2O.1 MN.7: 5 residues within 4Å: Chain B: N.147, H.169, E.210 Ligands: FMN.5, K.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.169, B:E.210, H2O.3, H2O.3 MN.11: 5 residues within 4Å: Chain C: N.147, H.169, E.210 Ligands: FMN.9, K.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.169, C:E.210, H2O.5 MN.15: 5 residues within 4Å: Chain D: N.147, H.169, E.210 Ligands: FMN.13, K.14 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.169, D:E.210, H2O.6, H2O.7 MN.19: 5 residues within 4Å: Chain E: N.147, H.169, E.210 Ligands: FMN.17, K.18 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.169, E:E.210, H2O.8, H2O.8 MN.23: 5 residues within 4Å: Chain F: N.147, H.169, E.210 Ligands: FMN.21, K.22 4 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:H.169, F:E.210, H2O.9, FMN.21

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: R.385, D.391, D.418, T.420 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.391, A:D.418, A:T.420 CA.8: 4 residues within 4Å: Chain B: R.385, D.391, D.418, T.420 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:R.385, B:D.391, B:D.418, B:T.420 CA.12: 4 residues within 4Å: Chain C: R.385, D.391, D.418, T.420 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:R.385, C:D.391, C:D.418, C:T.420, H2O.4 CA.16: 4 residues within 4Å: Chain D: R.385, D.391, D.418, T.420 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:R.385, D:D.391, D:D.418, D:T.420 CA.20: 4 residues within 4Å: Chain E: R.385, D.391, D.418, T.420 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:R.385, E:D.391, E:D.418, E:T.420, H2O.8 CA.24: 4 residues within 4Å: Chain F: R.385, D.391, D.418, T.420 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:R.385, F:D.391, F:D.418, F:T.420

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, K.A.P. et al., Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (FDCA). Acs Catalysis (2019)

Release Date

2019-02-27

Peptides

3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases