9FD4

flavin reductase ThdF in complex with two bound FADs in space group P212121

PDB DOI: https://doi.org/10.2210/pdb9FD4/pdb

Classification: FLAVOPROTEIN
Organism(s): Streptomyces albogriseolus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-16 Released: 2024-12-25
Deposition Author(s): Bork, S., Nagel, M.F., Keller, W., Niemann, H.H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.142
R-Value Work: 0.121
R-Value Observed: 0.122

Starting Models: 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

The NADH-dependent flavin reductase ThdF follows an ordered sequential mechanism though crystal structures reveal two FAD molecules in the active site

Horstmeier, H.J., Bork, S., Nagel, M.F., Keller, W., SproB, J., Diepold, N., Ruppel, M., Kottke, T., Niemann, H.H.

(null) Journal Of Biological Chemistry

Macromolecule Content

Total Structure Weight: 88.18 kDa
Atom Count: 6,319
Modelled Residue Count: 641
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin reductase	A, B [auth C], C [auth B], D	195	Streptomyces albogriseolus	Mutation(s): 0 Gene Names: thdF
UniProt
Find proteins for A0A1B1V585 (Streptomyces albogriseolus) Explore A0A1B1V585 Go to UniProtKB: A0A1B1V585
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1B1V585
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth D] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth D] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] J [auth C] K [auth C] L [auth B] E [auth A], F [auth A], J [auth C], K [auth C], L [auth B], M [auth B], P [auth D], Q [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth D] Focus chain Q [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D]	G [auth A], H [auth A], I [auth A], N [auth B], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain R [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain S [auth D] MOL2 format, chain O [auth B] MOL2 format, chain S [auth D] mmCIF format, chain O [auth B] mmCIF format, chain S [auth D]	O [auth B], S [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain S [auth D] Interactions & Density Focus chain O [auth B] Focus chain S [auth D]