2VR2

Human Dihydropyrimidinase

PDB DOI: https://doi.org/10.2210/pdb2VR2/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-25 Released: 2008-04-01
Deposition Author(s): Welin, M., Karlberg, T., Andersson, J., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wikstrom, M., Nordlund, P., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.251
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of Human Dihydropyrimidinase

Welin, M., Karlberg, T., Andersson, J., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Wikstrom, M., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 59.43 kDa
Atom Count: 3,697
Modelled Residue Count: 478
Deposited Residue Count: 541
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPYRIMIDINASE	A	541	Homo sapiens	Mutation(s): 0 EC: 3.5.2.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14117 (Homo sapiens) Explore Q14117 Go to UniProtKB: Q14117
PHAROS: Q14117 GTEx: ENSG00000147647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14117
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.251
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.65	α = 90
b = 89.65	β = 90
c = 219.1	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2015-05-06
Changes: Structure summary
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description