9V67 | pdb_00009v67

The crystal structure of a ThDP-dependent enzyme PpBFD

PDB DOI: https://doi.org/10.2210/pdb9V67/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-26 Released: 2026-06-03
Deposition Author(s): Hou, X.L., Zhou, J.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.229 (Depositor), 0.228 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Enantioselective C(sp3)-C(sp3) bond formation by synergistic thiamine-dependent radical biocatalysis and photoredox catalysis

Chun, J., Bao, Y., Zhang, Q., Hou, X., Wu, Z., Sun, H., Xing, Z., Chen, B., Zhang, Z., Zhao, Y., Zhou, J., Wang, B., Huang, X.

(2026) Nat Catal 9: 414-423

DOI: https://doi.org/10.1038/s41929-026-01515-w

Macromolecule Content

Total Structure Weight: 230.17 kDa
Atom Count: 16,874
Modeled Residue Count: 2,057
Deposited Residue Count: 2,120
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoylformate decarboxylase	A, B, C, D	530	Pseudomonas putida	Mutation(s): 0 Gene Names: mdlC EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida) Explore P20906 Go to UniProtKB: P20906
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20906
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain EB [auth D] SDF format, chain S [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain S [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain EB [auth D] mmCIF format, chain S [auth A]	AB [auth C], EB [auth D], S [auth A]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain AB [auth C] Focus chain EB [auth D] Focus chain S [auth A] Interactions & Density Focus chain AB [auth C] Focus chain EB [auth D] Focus chain S [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain DB [auth D] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain DB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	DB [auth D] HA [auth B] IA [auth B] JA [auth B] P [auth A] DB [auth D], HA [auth B], IA [auth B], JA [auth B], P [auth A], Q [auth A], R [auth A], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain DB [auth D] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain FB [auth D] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain KA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain FB [auth D] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain KA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain FB [auth D] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain KA [auth B]	BB [auth C] FB [auth D] KA [auth B] LA [auth B] MA [auth B] BB [auth C], FB [auth D], KA [auth B], LA [auth B], MA [auth B], T [auth A], U [auth A], V [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth C] Focus chain FB [auth D] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain BB [auth C] Focus chain FB [auth D] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain VA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain VA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain VA [auth C]	GA [auth B], VA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth B] Focus chain VA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain VA [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain SA [auth C] SDF format, chain UA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain TA [auth C] SDF format, chain RA [auth C] SDF format, chain OA [auth C] SDF format, chain N [auth A] SDF format, chain H [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain H [auth A]	AA [auth B] BA [auth B] CA [auth B] CB [auth D] DA [auth B] AA [auth B], BA [auth B], CA [auth B], CB [auth D], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], UA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] 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 CB [auth D] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]