SMTL ID : 9kti.1

CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in substrate bound form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

10 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.10, H.53, H.179, E.271 Ligands: 01.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.10, A:H.53, A:E.271, A:E.271 FE2.3: 5 residues within 4Å: Chain B: H.10, H.53, H.179, E.271 Ligands: 01.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.10, B:H.53, B:E.271, B:E.271 FE2.6: 5 residues within 4Å: Chain C: H.10, H.53, H.179, E.271 Ligands: 01.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.10, C:H.53, C:E.271, C:E.271 FE2.7: 5 residues within 4Å: Chain D: H.10, H.53, H.179, E.271 Ligands: 01.8 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.10, D:E.271, D:E.271 FE2.9: 5 residues within 4Å: Chain E: H.10, H.53, H.179, E.271 Ligands: 01.10 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.10, E:H.53, E:E.271, E:E.271 FE2.11: 5 residues within 4Å: Chain F: H.10, H.53, H.179, E.271 Ligands: 01.12 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.10, F:H.53, F:E.271, F:E.271 FE2.13: 5 residues within 4Å: Chain G: H.10, H.53, H.179, E.271 Ligands: 01.14 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.10, G:H.53, G:E.271, G:E.271 FE2.15: 5 residues within 4Å: Chain H: H.10, H.53, H.179, E.271 Ligands: 01.16 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.10, H:H.53, H:E.271, H:E.271 FE2.17: 5 residues within 4Å: Chain I: H.10, H.53, H.179, E.271 Ligands: 01.18 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.10, I:H.53, I:E.271, I:E.271 FE2.19: 5 residues within 4Å: Chain J: H.10, H.53, H.179, E.271 Ligands: 01.20 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.10, J:H.53, J:E.271, J:E.271

10 x 01: 3-[2,3-bis(oxidanyl)phenyl]propanoic acid

01.2: 10 residues within 4Å: Chain A: H.10, P.12, H.53, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.12, A:P.181, A:V.216, A:I.302 Hydrogen bonds: A:H.10, A:H.53 Salt bridges: A:H.115, A:R.212 01.4: 11 residues within 4Å: Chain B: P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:H.53, B:F.77, B:P.181, B:P.181, B:V.216, B:I.302 Hydrogen bonds: B:H.53 Salt bridges: B:H.115, B:R.212 01.5: 12 residues within 4Å: Chain C: H.10, P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.6 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:P.12, C:H.53, C:F.77, C:P.181, C:P.181, C:V.216, C:I.302 Hydrogen bonds: C:H.53, C:N.55 Salt bridges: C:H.53, C:H.115, C:R.212 01.8: 10 residues within 4Å: Chain D: H.10, P.12, H.53, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.7 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:P.12, D:P.181, D:P.181, D:V.216, D:I.302 Hydrogen bonds: D:H.10, D:H.53 Salt bridges: D:H.115, D:R.212 01.10: 10 residues within 4Å: Chain E: H.10, P.12, H.53, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.9 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:P.12, E:P.181, E:P.181, E:V.216, E:I.302 Hydrogen bonds: E:H.10, E:H.53 Salt bridges: E:H.115, E:R.212 01.12: 11 residues within 4Å: Chain F: P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.11 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:H.53, F:P.181, F:V.216, F:V.216, F:I.302 Hydrogen bonds: F:H.53, F:N.55, F:D.76 Salt bridges: F:R.212 01.14: 11 residues within 4Å: Chain G: P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.13 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:H.53, G:F.77, G:P.181, G:V.216, G:V.216, G:I.302 Hydrogen bonds: G:N.55, G:D.76 Salt bridges: G:H.115, G:R.212 01.16: 11 residues within 4Å: Chain H: P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.15 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:H.53, H:P.181, H:V.216, H:V.216, H:I.302 Hydrogen bonds: H:H.53, H:N.55, H:D.76 Salt bridges: H:R.212 01.18: 10 residues within 4Å: Chain I: P.12, H.53, N.55, D.76, F.77, H.115, P.181, V.216, I.302 Ligands: FE2.17 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:H.53, I:F.77, I:P.181, I:V.216, I:V.216, I:I.302 Hydrogen bonds: I:N.55, I:D.76 Salt bridges: I:H.115 01.20: 11 residues within 4Å: Chain J: P.12, H.53, N.55, D.76, F.77, H.115, P.181, R.212, V.216, I.302 Ligands: FE2.19 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:H.53, J:F.77, J:P.181, J:V.216, J:V.216, J:I.302 Hydrogen bonds: J:H.53, J:N.55, J:D.76 Salt bridges: J:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, X. et al., Structural and catalytic insights into MhpB: A dioxygenase enzyme for degrading catecholic pollutants. J Hazard Mater (2025)

Release Date

2025-02-12

Peptides

2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase

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