8CSO | pdb_00008cso

Crystal Structure of Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Uridine-5'-monophosphate

PDB DOI: https://doi.org/10.2210/pdb8CSO/pdb

Classification: LYASE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-13 Released: 2022-06-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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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 Orotidine 5'-phosphate decarboxylase from Klebsiella pneumoniae in complex with Guanosine-5'-monophosphate

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 258.67 kDa
Atom Count: 16,033
Modeled Residue Count: 2,191
Deposited Residue Count: 2,360
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	236	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0 Gene Names: pyrF, KPHS_21850 EC: 4.1.1.23
UniProt
Find proteins for A0A0H3GNE4 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GNE4 Go to UniProtKB: A0A0H3GNE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GNE4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P (Subject of Investigation/LOI) Query on U5P Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A], L [auth B], N [auth C], P [auth E], R [auth F]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth E] Focus chain R [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain O [auth C] SDF format, chain M [auth B] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B]	M [auth B], O [auth C], Q [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth F] Interactions & Density Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth F]