Protein profile

KP13_03218

Glutamate synthase [NADPH] small chain

Genome: KpKP13

Gene: AHE42458.1 gltD Structure source: AlphaFold + ColabFold UniProt A0A0H3GW91
Export view
Amino acids 472
Annotations 7
Features 28
PDB binders 5
Druggability 0.767

Overview

Basic information about this protein and its source genome.

Accession
KP13_03218
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42458.1 gltD
Status
annotated
Amino acids
472
Structure source
AlphaFold + ColabFold
EC
1.4.1.13
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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. 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:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.625
Human E-value
4.1e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
68.23
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.41

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 0.767
Structure A0A0H3GW91
Pocket Pocket 1
P2Rank 0.954
Structure A0A0H3GW91
Pocket Pocket 1
ColabFold model
FPocket 0.994 · Pocket 1
P2Rank 0.947 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 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 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • 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:0006537 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
25 134 Pfam PF14691 Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
25 134 InterPro IPR028261 Dihydroprymidine dehydrogenase domain II
145 269 Gene3D G3DSA:3.50.50.60 -
145 269 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
318 338 Coils Coil Coil
374 470 Gene3D G3DSA:3.50.50.60 -
374 470 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
10 144 Gene3D G3DSA:1.10.1060.10 -
10 144 InterPro IPR009051 Alpha-helical ferredoxin
324 337 PRINTS PR00419 Adrenodoxin reductase family signature
148 170 PRINTS PR00419 Adrenodoxin reductase family signature
171 184 PRINTS PR00419 Adrenodoxin reductase family signature
290 304 PRINTS PR00419 Adrenodoxin reductase family signature
213 223 PRINTS PR00419 Adrenodoxin reductase family signature
38 69 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
38 69 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
146 267 FunFam G3DSA:3.50.50.60:FF:000077 Glutamate synthase small subunit
7 157 SUPERFAMILY SSF46548 alpha-helical ferredoxin
145 401 SUPERFAMILY SSF51971 Nucleotide-binding domain
148 459 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
148 459 InterPro IPR023753 FAD/NAD(P)-binding domain
276 373 Gene3D G3DSA:3.50.50.60 -
276 373 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
285 472 FunFam G3DSA:3.50.50.60:FF:000068 Glutamate synthase small subunit
9 145 FunFam G3DSA:1.10.1060.10:FF:000004 Glutamate synthase, small subunit
6 472 NCBIfam TIGR01318 glutamate synthase, small subunit
6 472 InterPro IPR006006 Glutamate synthase NADPH small chain-like
3 471 PANTHER PTHR42783 GLUTAMATE SYNTHASE [NADPH] SMALL CHAIN

3D Structure

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

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GW91
AlphaFold — — full sequence — Viewing
ColabFold KP13_03218
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 0.767

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 21.69 0.873
2 4.7 0.206
3 4.6 0.199
4 4.12 0.166
5 2.69 0.08

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.

33 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
AKG
2VDC
Q05756 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
F3S
2VDC
Q05756 295.8 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]2S[Fe]3[S]2[Fe]1S3
FES
5VJ7
I6V148 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
MDE
1PS9
P42593 994.9 Da LogP 0.91 TPSA 382.6 3 viol. ✓ Clean CCCCC[C@@H](C\C=C\C(=O)SCCNC(=O)CCNC(C(=O)C(C)(…
OMT
2VDC
Q05756 181.2 Da LogP -1.17 TPSA 97.5 ✓ Ro5 ✓ Clean CS(=O)(=O)CC[C@@H](C(=O)O)N

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.