5NYB

A C145A mutant of Nesterenkonia AN1 amidase bound to adipamide

PDB DOI: https://doi.org/10.2210/pdb5NYB/pdb

Classification: HYDROLASE
Organism(s): Nesterenkonia sp. 10004
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-05-11 Released: 2018-06-13
Deposition Author(s): Kimani, S.W., Sewell, B.T.
Funding Organization(s): National Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.215
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

Substrate recognition by an amidase of the nitrilase superfamily

Kimani, S.W., Venter, G.A., Sewell, B.T.

To be published.

Macromolecule Content

Total Structure Weight: 30.21 kDa
Atom Count: 2,040
Modelled Residue Count: 262
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase	A	283	Nesterenkonia sp. 10004	Mutation(s): 1 Gene Names: Nit2 EC: 3.5.1.4
UniProt
Find proteins for D0VWZ1 (Nesterenkonia sp. 10004) Explore D0VWZ1 Go to UniProtKB: D0VWZ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9EE Query on 9EE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	adipamide C₆ H₁₂ N₂ O₂ GVNWZKBFMFUVNX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.215
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.254	α = 90
b = 114.769	β = 90
c = 64.842	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation	South Africa	91532

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.