1UF7

Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid amidohydrolase complexed with N-carbamyl-D-valine

PDB DOI: https://doi.org/10.2210/pdb1UF7/pdb

Classification: HYDROLASE
Organism(s): Agrobacterium sp.
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-05-26 Released: 2004-06-08
Deposition Author(s): Hashimoto, H., Aoki, M., Shimizu, T., Nakai, T., Morikawa, H., Ikenaka, Y., Takahashi, S., Sato, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.170 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid amidohydrolase

Hashimoto, H., Aoki, M., Shimizu, T., Nakai, T., Morikawa, H., Ikenaka, Y., Takahashi, S., Sato, M.

To be published.

Macromolecule Content

Total Structure Weight: 68.6 kDa
Atom Count: 5,522
Modelled Residue Count: 606
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-carbamyl-D-amino acid amidohydrolase	A, B	303	Agrobacterium sp.	Mutation(s): 2 EC: 3.5.1.77
UniProt
Find proteins for P60327 (Agrobacterium sp. (strain KNK712)) Explore P60327 Go to UniProtKB: P60327
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60327
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDV Query on CDV Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	3-METHYL-2-UREIDO-BUTYRIC ACID C₆ H₁₂ N₂ O₃ JDXMIYHOSFNZKO-SCSAIBSYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.170 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.452	α = 90
b = 137.696	β = 90
c = 68.024	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-08
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-12-27
Changes: Data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.