8DU1 | pdb_00008du1

Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis

PDB DOI: https://doi.org/10.2210/pdb8DU1/pdb

Classification: LYASE
Organism(s): Elizabethkingia anophelis NUHP1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-26 Released: 2022-08-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.155 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis

DeBouver, N.D., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 171.61 kDa
Atom Count: 13,126
Modeled Residue Count: 1,432
Deposited Residue Count: 1,468
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-glucose 4,6-dehydratase	A, B, C, D	367	Elizabethkingia anophelis NUHP1	Mutation(s): 0 Gene Names: BD94_3274 EC: 4.2.1.46
UniProt
Find proteins for A0A077ELH2 (Elizabethkingia anophelis NUHP1) Explore A0A077ELH2 Go to UniProtKB: A0A077ELH2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A077ELH2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], Q [auth C], W [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] G [auth A] H [auth A] J [auth B] L [auth B] E [auth A], G [auth A], H [auth A], J [auth B], L [auth B], M [auth B], P [auth C], R [auth C], S [auth C], V [auth D], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain X [auth D] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], T [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain O [auth C] MOL2 format, chain U [auth D] MOL2 format, chain O [auth C] mmCIF format, chain U [auth D] mmCIF format, chain O [auth C]	O [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain O [auth C] Focus chain U [auth D]