5MH6 | pdb_00005mh6

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)

PDB DOI: https://doi.org/10.2210/pdb5MH6/pdb

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

Deposited: 2016-11-23 Released: 2018-06-06
Deposition Author(s): Bisson, C., Baker, P.J., Domenech Perez, J., Pramanpol, N., Harding, S.E., Rice, D.W., Ferrer, J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council, Wellcome Trust, Wolfson Foundation, University of Alicante

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.162 (Depositor), 0.170 (DCC)
R-Value Work:
0.126 (Depositor), 0.130 (DCC)
R-Value Observed:
0.128 (Depositor)

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: 139.03 kDa
Atom Count: 11,624
Modelled Residue Count: 1,228
Deposited Residue Count: 1,232
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, C, D	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 LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain XA [auth C] SDF format, chain KB [auth D] SDF format, chain S [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain KB [auth D] MOL2 format, chain S [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain KB [auth D] mmCIF format, chain S [auth A]	HA [auth B], KB [auth D], S [auth A], XA [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain HA [auth B] Focus chain KB [auth D] Focus chain S [auth A] Focus chain XA [auth C] Interactions & Density Focus chain HA [auth B] Focus chain KB [auth D] Focus chain S [auth A] Focus chain XA [auth C]
7N5 Query on 7N5 Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain YA [auth C] SDF format, chain IA [auth B] SDF format, chain LB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain LB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain LB [auth D]	IA [auth B], LB [auth D], T [auth A], YA [auth C]	2-Ketohexanoic acid C₆ H₁₀ O₃ XNIHZNNZJHYHLC-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain LB [auth D] Focus chain T [auth A] Focus chain YA [auth C] Interactions & Density Focus chain IA [auth B] Focus chain LB [auth D] Focus chain T [auth A] Focus chain YA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain EB [auth D] SDF format, chain QA [auth C] SDF format, chain K [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain QA [auth C] MOL2 format, chain K [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain QA [auth C] mmCIF format, chain K [auth A]	BA [auth B], EB [auth D], K [auth A], QA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain EB [auth D] Focus chain K [auth A] Focus chain QA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain EB [auth D] Focus chain K [auth A] Focus chain QA [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain CB [auth D] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain NA [auth C] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain BB [auth D] SDF format, chain DB [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain DB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain DB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	AA [auth B] AB [auth D] BB [auth D] CB [auth D] DB [auth D] AA [auth B], AB [auth D], BB [auth D], CB [auth D], DB [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] 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 KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] 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] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DB [auth D] 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 KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] 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]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain JB [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain WA [auth C] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain RA [auth C] SDF format, chain U [auth A] SDF format, chain VA [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain JB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth C]	CA [auth B] DA [auth B] EA [auth B] FA [auth B] FB [auth D] CA [auth B], DA [auth B], EA [auth B], FA [auth B], FB [auth D], GA [auth B], GB [auth D], HB [auth D], IB [auth D], JB [auth D], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], RA [auth C], SA [auth C], TA [auth C], U [auth A], UA [auth C], VA [auth C], WA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain ZA [auth D] MOL2 format, chain JA [auth C] MOL2 format, chain ZA [auth D] mmCIF format, chain JA [auth C] mmCIF format, chain ZA [auth D]	JA [auth C], ZA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain JA [auth C] Focus chain ZA [auth D] Interactions & Density Focus chain JA [auth C] Focus chain ZA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.162 (Depositor), 0.170 (DCC)
R-Value Work: 0.126 (Depositor), 0.130 (DCC)
R-Value Observed: 0.128 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.455	α = 109.11
b = 75.008	β = 107.55
c = 77.555	γ = 95.91

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 2.0: 2024-06-19
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy