3KB6 | pdb_00003kb6

Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid

PDB DOI: https://doi.org/10.2210/pdb3KB6/pdb
Entry: 3KB6 supersedes: 2PI1

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-20 Released: 2009-11-10
Deposition Author(s): Antonyuk, S.V., Strange, R.W., Ellis, M.J., Bessho, Y., Kuramitsu, S., Yokoyama, S., Hasnain, S.S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.164 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

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

Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).

Antonyuk, S.V., Strange, R.W., Ellis, M.J., Bessho, Y., Kuramitsu, S., Inoue, Y., Yokoyama, S., Hasnain, S.S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1209-1213

PubMed: 20054113 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309109044935
Primary Citation of Related Structures:
3KB6

PubMed Abstract:
The crystal structure of D-lactate dehydrogenase from Aquifex aeolicus (aq_727) was determined to 2.12 A resolution in space group P2(1)2(1)2(1), with unit-cell parameters a = 90.94, b = 94.43, c = 188.85 A. The structure was solved by molecular replacement using the coenzyme-binding domain of Lactobacillus helveticus D-lactate dehydrogenase and contained two homodimers in the asymmetric unit. Each subunit of the homodimer was found to be in a ;closed' conformation with the NADH cofactor bound to the coenzyme-binding domain and with a lactate (or pyruvate) molecule bound at the interdomain active-site cleft.

Organizational Affiliation

Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England.

Macromolecule Content

Total Structure Weight: 161.2 kDa
Atom Count: 12,114
Modelled Residue Count: 1,335
Deposited Residue Count: 1,336
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lactate dehydrogenase	A, B, C, D	334	Aquifex aeolicus	Mutation(s): 0 Gene Names: aq_727, ldhA EC: 1.1.1.28
UniProt
Find proteins for O66939 (Aquifex aeolicus (strain VF5)) Explore O66939 Go to UniProtKB: O66939
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66939
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 G [auth A] SDF format, chain JA [auth C] SDF format, chain QA [auth D] SDF format, chain Y [auth B] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain Y [auth B]	G [auth A], JA [auth C], QA [auth D], Y [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain Y [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain FA [auth B] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain Q [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A]	AA [auth B] BA [auth B] FA [auth B] I [auth A] L [auth A] AA [auth B], BA [auth B], FA [auth B], I [auth A], L [auth A], LA [auth C], N [auth A], Q [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain I [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain N [auth A] Focus chain Q [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain I [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain N [auth A] Focus chain Q [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth C] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A]	GA [auth C] H [auth A] K [auth A] M [auth A] NA [auth C] GA [auth C], H [auth A], K [auth A], M [auth A], NA [auth C], R [auth A], S [auth A], T [auth A], TA [auth D], U [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain NA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Interactions & Density Focus chain GA [auth C] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain NA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain V [auth B] SDF format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth B]	CA [auth B] DA [auth B] EA [auth B] KA [auth C] MA [auth C] CA [auth B], DA [auth B], EA [auth B], KA [auth C], MA [auth C], O [auth A], P [auth A], RA [auth D], SA [auth D], V [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain V [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain V [auth B] Focus chain Z [auth B]
LAC Query on LAC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain X [auth B] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain X [auth B]	F [auth A], IA [auth C], PA [auth D], X [auth B]	LACTIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-UWTATZPHSA-N		Interactions Focus chain F [auth A] Focus chain IA [auth C] Focus chain PA [auth D] Focus chain X [auth B] Interactions & Density Focus chain F [auth A] Focus chain IA [auth C] Focus chain PA [auth D] Focus chain X [auth B]
PPI Query on PPI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain OA [auth D] SDF format, chain W [auth B] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain E [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain W [auth B]	E [auth A], HA [auth C], J [auth A], OA [auth D], W [auth B]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth C] Focus chain J [auth A] Focus chain OA [auth D] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain HA [auth C] Focus chain J [auth A] Focus chain OA [auth D] Focus chain W [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.164 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.938	α = 90
b = 94.432	β = 90
c = 188.849	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

This entry supersedes: 2PI1

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 1.3: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection