9J2L | pdb_00009j2l

4,5-DOPA-extradiol-dioxygenase from Mirabilis jalapa

PDB DOI: https://doi.org/10.2210/pdb9J2L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mirabilis jalapa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-07 Released: 2025-08-13
Deposition Author(s): Chou, Y.C., Hsu, C.H.
Funding Organization(s): National Science Council (NSC, Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.147 (Depositor), 0.148 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure-guided design of the dopamine biocatalyst from DOPA dioxygenase

Yeh, Y.C., Hsu, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 97.43 kDa
Atom Count: 6,867
Modeled Residue Count: 791
Deposited Residue Count: 825
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4,5-DOPA dioxygenase extradiol	A, B, C	275	Mirabilis jalapa	Mutation(s): 0 Gene Names: DOD EC: 1.13.11.29
UniProt
Find proteins for B6F0W8 (Mirabilis jalapa) Explore B6F0W8 Go to UniProtKB: B6F0W8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6F0W8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain EA [auth C] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain S [auth B]	D [auth A], EA [auth C], S [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain EA [auth C] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain EA [auth C] Focus chain S [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain U [auth B]	F [auth A], U [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain U [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain DA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain V [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain GA [auth C] SDF format, chain CA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain V [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain V [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain CA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] G [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], P [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain FA [auth C] SDF format, chain E [auth A] MOL2 format, chain T [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain T [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain E [auth A]	E [auth A], FA [auth C], T [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain T [auth B]