5UE9 | pdb_00005ue9

WT DHODB with orotate bound

PDB DOI: https://doi.org/10.2210/pdb5UE9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-29 Released: 2017-09-06
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.254 (Depositor), 0.259 (DCC)
R-Value Work:
0.195 (Depositor), 0.201 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Isoleucine 74 Plays a Key Role in Controlling Electron Transfer Between Lactococcus lactis Dihydroorotate Dehydrogenase 1B Subunits

Pompeu, Y.A., Stewart, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 125.78 kDa
Atom Count: 8,957
Modeled Residue Count: 1,135
Deposited Residue Count: 1,136
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase	A, D [auth C]	306	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: pyrD, NCDO895_2365 EC: 1.3.1.14
UniProt
Find proteins for Q9CFW8 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW8 Go to UniProtKB: Q9CFW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CFW8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit	B, C [auth D]	262	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: pyrK, NCDO895_2366
UniProt
Find proteins for Q9CFW7 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CFW7 Go to UniProtKB: Q9CFW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CFW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain H [auth B]	H [auth B], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain E [auth A]	E [auth A], M [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth C]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth B] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B]	I [auth B], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth D]
ORO Query on ORO Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain F [auth A]	F [auth A], N [auth C]	OROTIC ACID C₅ H₄ N₂ O₄ PXQPEWDEAKTCGB-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B]	J [auth B], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain J [auth B] Focus chain O [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]