6ZE6

FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-nitrocatechol

PDB DOI: https://doi.org/10.2210/pdb6ZE6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2020-06-16 Released: 2021-05-26
Deposition Author(s): Svecova, L., Skalova, T., Kolenko, P., Koval, T., Oestergaard, L.H., Dohnalek, J.
Funding Organization(s): European Regional Development Fund, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.147
R-Value Work: 0.113
R-Value Observed: 0.114

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 133.89 kDa
Atom Count: 11,641
Modelled Residue Count: 1,169
Deposited Residue Count: 1,190
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-dependent oxidoreductase	A, B	595	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0048040
UniProt
Find proteins for G0SAW6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SAW6 Go to UniProtKB: G0SAW6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0SAW6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA (Subject of Investigation/LOI) Query on FDA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain S [auth B]	E [auth A], S [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
4NC (Subject of Investigation/LOI) Query on 4NC Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	K [auth A], L [auth A], X [auth B], Y [auth B]	4-NITROCATECHOL C₆ H₅ N O₄ XJNPNXSISMKQEX-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth B]	AA [auth B], M [auth A], N [auth A], Z [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	BA [auth B], O [auth A], P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain BA [auth B] Focus chain O [auth A] Focus chain P [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A]	R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.147
R-Value Work: 0.113
R-Value Observed: 0.114
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.15785/SBGRID/808

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.565	α = 90
b = 109.746	β = 90
c = 116.071	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Funding Organization	Location	Grant Number
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/15_003/0000447
European Regional Development Fund	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0109
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2015043
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2018127
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LQ1604

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2021-06-16
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description