7DQX | pdb_00007dqx

Crystal structure of xanthine dehydrogenase family protein

PDB DOI: https://doi.org/10.2210/pdb7DQX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paenarthrobacter nicotinovorans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-24 Released: 2022-01-26
Deposition Author(s): Lei, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.44 Å
R-Value Free:
0.326 (Depositor), 0.330 (DCC)
R-Value Work:
0.287 (Depositor), 0.290 (DCC)
R-Value Observed:
0.289 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

crystal structure of xanthine dehydrogenase family protein

Lei, W.

To be published.

Macromolecule Content

Total Structure Weight: 275.07 kDa
Atom Count: 18,678
Modeled Residue Count: 2,435
Deposited Residue Count: 2,500
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxypseudooxynicotine dehydrogenase complex subunit gamma	A, F [auth D]	794	Paenarthrobacter nicotinovorans	Mutation(s): 0 Gene Names: kdhC, kdhL EC: 1.5.99.14
UniProt
Find proteins for Q933N0 (Paenarthrobacter nicotinovorans) Explore Q933N0 Go to UniProtKB: Q933N0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q933N0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha	B	296	Paenarthrobacter nicotinovorans	Mutation(s): 0 Gene Names: kdhA, kdhM EC: 1.5.99.14
UniProt
Find proteins for O87681 (Paenarthrobacter nicotinovorans) Explore O87681 Go to UniProtKB: O87681
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O87681
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxypseudooxynicotine dehydrogenase complex subunit beta	C, E [auth F]	160	Paenarthrobacter nicotinovorans	Mutation(s): 0 Gene Names: kdhB, kdhS EC: 1.5.99.14
UniProt
Find proteins for O87682 (Paenarthrobacter nicotinovorans) Explore O87682 Go to UniProtKB: O87682
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O87682
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha	D [auth E]	296	Paenarthrobacter nicotinovorans	Mutation(s): 0 Gene Names: kdhA, kdhM EC: 1.5.99.14
UniProt
Find proteins for O87681 (Paenarthrobacter nicotinovorans) Explore O87681 Go to UniProtKB: O87681
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O87681
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth E] MOL2 format, chain I [auth B] MOL2 format, chain L [auth E] mmCIF format, chain I [auth B] mmCIF format, chain L [auth E]	I [auth B], L [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain I [auth B] Focus chain L [auth E] Interactions & Density Focus chain I [auth B] Focus chain L [auth E]
MCN Query on MCN Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain G [auth A] MOL2 format, chain O [auth D] MOL2 format, chain G [auth A] mmCIF format, chain O [auth D] mmCIF format, chain G [auth A]	G [auth A], O [auth D]	PTERIN CYTOSINE DINUCLEOTIDE C₁₉ H₂₂ N₈ O₁₃ P₂ S₂ RBWYFPNWTRZKKZ-LOIMWUFNSA-N		Interactions Focus chain G [auth A] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain O [auth D]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth F] SDF format, chain N [auth F] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F]	J [auth C], K [auth C], M [auth F], N [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth F] Focus chain N [auth F] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth F] Focus chain N [auth F]
MO Query on MO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth D] MOL2 format, chain H [auth A] MOL2 format, chain P [auth D] mmCIF format, chain H [auth A] mmCIF format, chain P [auth D]	H [auth A], P [auth D]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain P [auth D]