5MH5

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)

PDB DOI: https://doi.org/10.2210/pdb5MH5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Haloferax mediterranei ATCC 33500
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-23 Released: 2018-05-02
Deposition Author(s): Bisson, C., Baker, P.J., Domenech Perez, J., Pramanpol, N., Harding, S.E., Rice, D.W., Ferrer, J.
Funding Organization(s): University of Alicante, Biotechnology and Biological Sciences Research Council, Wellcome Trust, Wolfson Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.167
R-Value Work: 0.136
R-Value Observed: 0.137

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Productive ternary complexes of D-2-hydroxyacid dehydrogenase provide insights into the chiral specificity of its reaction mechanism

Domenech Perez, J., Pramanpol, N., Baker, P.J., Bisson, C., Harding, S.E., Rice, D.W., Ferrer, J.

To be published.

Macromolecule Content

Total Structure Weight: 69.19 kDa
Atom Count: 5,605
Modelled Residue Count: 616
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-2-hydroxyacid dehydrogenase	A, B	308	Haloferax mediterranei ATCC 33500	Mutation(s): 0 Gene Names: ddh, serA5, HFX_2024 EC: 1.1.1
UniProt
Find proteins for Q2VEQ7 (Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4)) Explore Q2VEQ7 Go to UniProtKB: Q2VEQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2VEQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain P [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain P [auth A]	BA [auth B], P [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain BA [auth B] Focus chain P [auth A]
7N5 Query on 7N5 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain O [auth A]	AA [auth B], O [auth A]	2-Ketohexanoic acid C₆ H₁₀ O₃ XNIHZNNZJHYHLC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain O [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain Q [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain Q [auth A]	CA [auth B], Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain Q [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.167
R-Value Work: 0.136
R-Value Observed: 0.137
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.53	α = 90
b = 87.4	β = 96.34
c = 66.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
University of Alicante	Spain	VIGROB046
Biotechnology and Biological Sciences Research Council	United Kingdom	--
Wellcome Trust	United Kingdom	--
Wolfson Foundation	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 2.0: 2024-02-14
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy