3BGJ

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

PDB DOI: https://doi.org/10.2210/pdb3BGJ/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-26 Released: 2008-11-18
Deposition Author(s): Liu, Y., Tang, H.L., Bello, A.M., Devalla, S., Kotra, L.P., Pai, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.209
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

Liu, Y., Tang, H.L., Bello, A.M., Devalla, S., Kotra, L.P., Pai, E.F.

To be published.

Macromolecule Content

Total Structure Weight: 64.24 kDa
Atom Count: 4,347
Modelled Residue Count: 514
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A, B	291	Homo sapiens	Mutation(s): 0 Gene Names: UMPS EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens) Explore P11172 Go to UniProtKB: P11172
PHAROS: P11172 GTEx: ENSG00000114491
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.209
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.803	α = 90
b = 61.821	β = 111.66
c = 70.881	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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3BGJ

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)