5LOA

Crystal structure of the engineered D-Amino Acid Dehydrogenase (DAADH) bound to NADP+

PDB DOI: https://doi.org/10.2210/pdb5LOA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-09 Released: 2017-08-16
Deposition Author(s): Dunstan, M.S., Gahloth, D.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.206
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Single-biocatalyst synthesis of enantiopure D-arylalanines exploiting an engineered D-amino acid dehydrogenase

Parmeggiani, F., Ahmed, S.T., Thompson, M.P., Weise, N.J., Galman, J.L., Gahloth, D., Dunstan, M.S., Leys, D., Turner, N.J.

To be published.

Macromolecule Content

Total Structure Weight: 71.49 kDa
Atom Count: 5,499
Modelled Residue Count: 638
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meso-diaminopimelate D-dehydrogenase	A, B	319	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: ddh, Cgl2617, cg2900 EC: 1.4.1.16
UniProt
Find proteins for P04964 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore P04964 Go to UniProtKB: P04964
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP 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]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.206
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.02	α = 90
b = 64.58	β = 106.89
c = 82.06	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K00199X/1

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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.