Protein profile

VK055_3853

glutamate synthase (NADPH) large chain glutamatesynthase, large subunit

Genome: KpATCC43816

Gene: AIK82403.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GY60

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Amino acids 1448

Annotations 10

Features 33

PDB binders 4

Druggability 0.868

Overview

Basic information about this protein and its source genome.

Accession: VK055_3853
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82403.1
Status: annotated
Amino acids: 1448
Structure source: AlphaFold + ColabFold

1.4.1.13

GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0015930 Catalysis of the formation of L-glutamine and 2-oxoglutarate from L-glutamate, using NADH, NADPH or ferredoxin as hydrogen acceptors. GO:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid. GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GO:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 59.903
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.65

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 0.868

Structure A0A0H3GY60

Pocket Pocket 1

P2Rank 0.957

Structure A0A0H3GY60

Pocket Pocket 1

ColabFold model

FPocket 0.812 · Pocket 3

P2Rank 0.95 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 144 / 4744 genomes with a hit

Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

MQHRGAILADGKTGDGCGLLLQKPDRFFRIVAEERGWRLAKNYAVGMLFLNKDPELAKAARRIVEEELQLETLSIVGWRDVPTNEGVLGEIALSSLPRIEQIFVNAPAGWRPRDMERRLFIARRRIEKRLQEDKDFYVCSLSNLVNIYKGLCMPADLPRFYLDLADLRLESAICLFHQRFSTNTVPRWPLAQPFRYLAHNGEINTITGNRQWARARTYKFQTPLIPDLHDAAPFVNETGSDSSSMDNMLELLLAGGMDIVRAMRLLVPPAWQNNPDMDPELRSFFDFNSMHMEPWDGPAGIVMSDGRYAACNLDRNGLRPARYVITKDKLITCASEVGIWDYQPDEVVEKGRVGPGELMVIDTRAGRILHSAETDDDLKSRHPYKEWMEKNVRRLVPFEDLPDEEVGSRQLDDDTLASYQKQFNYSAEELDSVLRVLGENGQEAVGSMGDDTPFAVLSSQPRIIYDYFRQQFAQVTNPPIDPLREAHVMSLATSIGREMNVFCEAEGQAHRLSFKSPILLYSDFKQLTTMEEEHYRADVLDITFNPAEASLSETVKALCDKAEQMVRDGTVLLVLSDRNIAKDRLPVPAPMAVGAIQTRLVDKSLRCDANIIVETASARDPHHFAVLLGFGATAIYPYLAYETLAKLVDSKAIDKPYRAVMLNYRNGINKGLYKIMSKMGISTIASYRCSKLFEAVGLHRDVSDLCFQGVVSRIGGASFDDFQQDLLNLSKRAWLARKPLAQGGLLKYVHGGEYHAYNPDVVRTLQQAVQSGEYSDYQQYAKLVNERPAATLRDLLALNPGEDAISIDEVEPAKELFKRFDTAAMSIGALSPEAHESLAEAMNSIGGFSNSGEGGEDPARYGTNKVSRIKQVASGRFGVTPAYLVNADVIQIKVAQGAKPGEGGQLPGDKVTPYIAKLRYSVPGVTLISPPPHHDIYSIEDLAQLIFDLKQVNPKAMISVKLVSEPGVGTIATGVAKAYADLITIAGYDGGTGASPLSSVKYAGCPWELGLVETQQALVANGLRHKIRLQVDGGLKTGLDIIKAAILGAESFGFGTGPMVALGCKYLRICHLNNCATGVATQDDKLRKNHYHGLPFKVTNYFEFIARETRELMAQLGVKRLVDLIGRTDLLKELDGFTAKQQKLDLGKLLETAEPHPGKALYCTENNPPFDNGVLNAQLLQQAKPYVDEKQSKTFWFDIRNTDRSVGASLSGYIAQTHGDQGLAGDPIVAHFSGTAGQSFGVWNAGGVELHLTGDANDYVGKGMAGGLLAIRPPVGSAFRSHEASIIGNTCLYGATGGRLYAAGRAGERFAVRNSGAITVVEGIGDNGCEYMTGGIVCVLGKTGVNFGAGMTGGFAYVLDEDGDFRKRVNPELVEVLDVDSLAIHEEHLRGLITEHVQLTGSQRGEEILANWPAFSAKFALVKPKSSDVKALLGHRSRSAAELRVQAQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1.4.1.13

Gene Ontology (GO)

GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0015930 Catalysis of the formation of L-glutamine and 2-oxoglutarate from L-glutamate, using NADH, NADPH or ferredoxin as hydrogen acceptors.
GO:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GO:0051538 Binding to a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
GO:0004355 Catalysis of the reaction: 2 L-glutamate + NADP+ = 2-oxoglutarate + L-glutamine + H+ + NADPH. This is a two-step reaction: (a) L-glutamate + NH4+ = L-glutamine + H2O, (b) L-glutamate + NADP+ + H2O = NH4+ + 2-oxoglutarate + NADPH + H+.
GO:0046872 Binding to a metal ion.
GO:0019676 The pathway by which ammonia is processed and incorporated into a cell. In an energy-rich (glucose-containing), nitrogen-poor environment, glutamine synthetase and glutamate synthase form an ammonia assimilatory cycle, in which ammonia is incorporated into L-glutamate to form L-glutamine, which then combines with alpha-ketoglutarate to regenerate L-glutamate. This ATP-dependent cycle is essential for nitrogen-limited growth and for steady-state growth with some sources of nitrogen.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
1	387	Pfam	PF00310	Glutamine amidotransferases class-II
1	387	InterPro	IPR017932	Glutamine amidotransferase type 2 domain
758	1132	CDD	cd02808	GltS_FMN
758	1132	InterPro	IPR002932	Glutamate synthase domain
746	1157	FunFam	G3DSA:3.20.20.70:FF:000061	Glutamate synthase large subunit
1	391	SUPERFAMILY	SSF56235	N-terminal nucleophile aminohydrolases (Ntn hydrolases)
1	391	InterPro	IPR029055	Nucleophile aminohydrolases, N-terminal
1	506	Gene3D	G3DSA:3.60.20.10	Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
1	506	InterPro	IPR029055	Nucleophile aminohydrolases, N-terminal
1159	1429	Gene3D	G3DSA:2.160.20.60	-
1159	1429	InterPro	IPR036485	Glutamate synthase, alpha subunit, C-terminal domain superfamily
1173	1427	SUPERFAMILY	SSF69336	Alpha subunit of glutamate synthase, C-terminal domain
1173	1427	InterPro	IPR036485	Glutamate synthase, alpha subunit, C-terminal domain superfamily
1161	1429	FunFam	G3DSA:2.160.20.60:FF:000002	Glutamate synthase, large subunit
1198	1380	Pfam	PF01493	GXGXG motif
1198	1380	InterPro	IPR002489	Glutamate synthase, alpha subunit, C-terminal
419	699	Pfam	PF04898	Glutamate synthase central domain
419	699	InterPro	IPR006982	Glutamate synthase, central-N
396	1153	SUPERFAMILY	SSF51395	FMN-linked oxidoreductases
755	1118	Pfam	PF01645	Conserved region in glutamate synthase
755	1118	InterPro	IPR002932	Glutamate synthase domain
391	747	Gene3D	G3DSA:3.20.20.70	Aldolase class I
391	747	InterPro	IPR013785	Aldolase-type TIM barrel
444	1133	Gene3D	G3DSA:3.20.20.70	Aldolase class I
444	1133	InterPro	IPR013785	Aldolase-type TIM barrel
5	1428	PANTHER	PTHR11938	FAD NADPH DEHYDROGENASE/OXIDOREDUCTASE
1	364	ProSiteProfiles	PS51278	Glutamine amidotransferase type 2 domain profile.
1	364	InterPro	IPR017932	Glutamine amidotransferase type 2 domain
1	382	CDD	cd00713	GltS
1	397	FunFam	G3DSA:3.60.20.10:FF:000001	Glutamate synthase, large subunit
1175	1425	CDD	cd00982	gltB_C
1175	1425	InterPro	IPR002489	Glutamate synthase, alpha subunit, C-terminal
398	745	FunFam	G3DSA:3.20.20.70:FF:000109	Glutamate synthase, large subunit

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_A0A0H3GY60	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3853	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				0.868
4				0.711

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	26.42	0.913
2	8.91	0.477
3	8.17	0.435
4	8.09	0.431
5	6.91	0.356

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
3				0.812
10				0.713
11				0.258

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	24.34	0.898
2	14.66	0.73
3	11.42	0.61
4	9.27	0.497
5	7.73	0.409

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

30 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AKG	1LLW	P55038	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
F3S	1LLW	P55038	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
OMT	1EA0	Q05755	181.2 Da LogP -1.17 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=O)CC[C@@H](C(=O)O)N`
ONL	1OFE	P55038	145.2 Da LogP -0.23 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)CC[C@@H](C(=O)O)N`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC19429847	0.607	208.3 Da LogP -1.16 TPSA 80.5	✓ Ro5	✓ Clean	`CN(C)C(=O)[C@@H](N)CCS(C)(=O)=O`
ZINC19429848	0.607	208.3 Da LogP -1.16 TPSA 80.5	✓ Ro5	✓ Clean	`CN(C)C(=O)[C@H](N)CCS(C)(=O)=O`
ZINC26513844	0.607	209.3 Da LogP -0.69 TPSA 86.5	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](N)CCS(C)(=O)=O`
ZINC26513846	0.607	209.3 Da LogP -0.69 TPSA 86.5	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](N)CCS(C)(=O)=O`
ZINC3055005	0.565	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.565	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.565	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555366	0.542	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.542	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.542	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.542	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.542	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.542	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1643467	0.517	217.2 Da LogP -1.12 TPSA 117.7	✓ Ro5	✓ Clean	`CS(=O)(=O)CC[C@@H](N)P(=O)(O)O`
ZINC6425006	0.517	217.2 Da LogP -1.12 TPSA 117.7	✓ Ro5	✓ Clean	`CS(=O)(=O)CC[C@H](N)P(=O)(O)O`
ZINC34050079	0.516	224.2 Da LogP -0.91 TPSA 130.0	✓ Ro5	✓ Clean	`CS(=O)(=O)/N=C(\O)CC[C@H](N)C(=O)O`
ZINC1570993	0.500	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](N)C(=O)O`
ZINC1570999	0.500	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1620974	0.500	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC1742220	0.500	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@H](N)C(=O)O`
ZINC2035155	0.500	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](N)C(=O)O`
ZINC2035157	0.500	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](N)C(=O)O`
ZINC2037129	0.500	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC43531622	0.500	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](N)C(=O)O`
ZINC43531626	0.500	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](N)C(=O)O`
ZINC8437446	0.500	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](N)C(=O)O`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.