Protein profile

VK055_4953

D-lactate dehydrogenase

Genome: KpATCC43816

Gene: AIK83479.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW01

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Amino acids 581

Annotations 14

Features 31

PDB binders 0

Druggability 0.995

Overview

Basic information about this protein and its source genome.

Accession: VK055_4953
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83479.1
Status: annotated
Amino acids: 581
Structure source: AlphaFold + ColabFold

1.1.5.12

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0016901 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule. GO:0019516 OBSOLETE. The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons. GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 92.95

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.995

Structure A0A0H3GW01

Pocket Pocket 1

P2Rank 0.997

Structure A0A0H3GW01

Pocket Pocket 1

ColabFold model

FPocket 0.937 · Pocket 6

P2Rank 0.995 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 151 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1.1.5.12

Gene Ontology (GO)

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0016901 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
GO:0019516 OBSOLETE. The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0006089 The chemical reactions and pathways involving lactate, the anion of lactic acid.
GO:0031234 The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
GO:0004458 Catalysis of the reaction: (R)-lactate + 2 [Fe(III)cytochrome c] = 2 [Fe(II)cytochrome c] + 2 H+ + pyruvate.
GO:0102029 Catalysis of the reaction: (R)-lactate + an ubiquinone = pyruvate + an ubiquinol.
GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
269	353	FunFam	G3DSA:3.30.70.610:FF:000001	Quinone-dependent D-lactate dehydrogenase
276	567	SUPERFAMILY	SSF55103	FAD-linked oxidases, C-terminal domain
276	567	InterPro	IPR016164	FAD-linked oxidase-like, C-terminal
106	268	FunFam	G3DSA:3.30.465.10:FF:000015	Quinone-dependent D-lactate dehydrogenase
435	519	Gene3D	G3DSA:3.30.1370.20	-
435	519	InterPro	IPR016173	D-lactate dehydrogenase, cap domain, subdomain 2
435	519	FunFam	G3DSA:3.30.1370.20:FF:000001	Quinone-dependent D-lactate dehydrogenase
547	581	MobiDBLite	mobidb-lite	consensus disorder prediction
278	567	Pfam	PF09330	D-lactate dehydrogenase, membrane binding
278	567	InterPro	IPR015409	D-lactate dehydrogenase, membrane binding, C-terminal
10	271	SUPERFAMILY	SSF56176	FAD-binding/transporter-associated domain-like
10	271	InterPro	IPR036318	FAD-binding, type PCMH-like superfamily
1	103	Gene3D	G3DSA:3.30.43.10	-
1	103	InterPro	IPR016167	FAD-binding, type PCMH, subdomain 1
355	434	FunFam	G3DSA:3.30.70.610:FF:000002	Quinone-dependent D-lactate dehydrogenase
47	168	Pfam	PF01565	FAD binding domain
47	168	InterPro	IPR006094	FAD linked oxidase, N-terminal
4	569	PIRSF	PIRSF000101	D-lactate_dh
4	569	InterPro	IPR012256	D-lactate dehydrogenase
106	268	Gene3D	G3DSA:3.30.465.10	-
106	268	InterPro	IPR016169	FAD-binding, type PCMH, subdomain 2
269	352	Gene3D	G3DSA:3.30.70.610	-
269	352	InterPro	IPR016172	D-lactate dehydrogenase, cap domain, subdomain 1
353	434	Gene3D	G3DSA:3.30.70.610	-
353	434	InterPro	IPR016172	D-lactate dehydrogenase, cap domain, subdomain 1
42	272	ProSiteProfiles	PS51387	PCMH-type FAD-binding domain profile.
42	272	InterPro	IPR016166	FAD-binding domain, PCMH-type
2	103	FunFam	G3DSA:3.30.43.10:FF:000005	Quinone-dependent D-lactate dehydrogenase
9	557	PANTHER	PTHR43716	D-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL
10	568	Hamap	MF_02092	Quinone-dependent D-lactate dehydrogenase [dld].
10	568	InterPro	IPR012256	D-lactate dehydrogenase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GW01	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4953	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.995
13				0.655
16				0.233

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				70.68	0.991
2				1.17	0.009

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
6				0.937
38				0.59

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	60.95	0.988
2	10.35	0.556
3	0.82	0.003