Protein profile

KP13_02003

phosphoglycerate mutase

Genome: KpKP13

Gene: gpmB AHE46440.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMA1
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Amino acids 215
Annotations 6
Features 19
PDB binders 8
Druggability 0.86

Overview

Basic information about this protein and its source genome.

Accession
KP13_02003
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
gpmB AHE46440.1
Status
annotated
Amino acids
215
Structure source
AlphaFold + ColabFold
EC
5.4.2.-
GO
GO:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. 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:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.938
Human E-value
2.96e-14
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.31

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 0.86
Structure A0A0H3GMA1
Pocket Pocket 1
P2Rank 0.38
Structure A0A0H3GMA1
Pocket Pocket 1
ColabFold model
FPocket 0.762 · Pocket 1
P2Rank 0.791 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 111 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate.
  • 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:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
146 168 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 208 SUPERFAMILY SSF53254 Phosphoglycerate mutase-like
1 208 InterPro IPR029033 Histidine phosphatase superfamily
3 184 CDD cd07067 HP_PGM_like
3 184 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
6 15 ProSitePatterns PS00175 Phosphoglycerate mutase family phosphohistidine signature.
6 15 InterPro IPR001345 Phosphoglycerate/bisphosphoglycerate mutase, active site
4 194 Pfam PF00300 Histidine phosphatase superfamily (branch 1)
4 194 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
146 168 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
3 157 SMART SM00855 PGAM_5
3 157 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
169 215 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
3 187 PANTHER PTHR48100 BROAD-SPECIFICITY PHOSPHATASE YOR283W-RELATED
1 215 Hamap MF_01040 Probable phosphoglycerate mutase GpmB [gpmB].
1 215 InterPro IPR023086 Phosphoglycerate mutase, GpmB, probable
1 211 Gene3D G3DSA:3.40.50.1240 -
1 211 InterPro IPR029033 Histidine phosphatase superfamily
1 145 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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

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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_A0A0H3GMA1
AlphaFold — — full sequence — Viewing
ColabFold KP13_02003
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 0.86

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 3.07 0.102
2 1.8 0.034

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.

59 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
3PG
3GP5
Q3JWH7 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
AGS
1K6M
P16118 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
G3H
1C7Z
P07953 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C([C@H](C=O)O)OP(=O)(O)O
MLI
3LNT
Q3JWH7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PG6
3GP5
Q3JWH7 266.3 Da LogP 0.35 TPSA 55.4 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOC
PO3
3GP3
Q3JWH7 79.0 Da LogP -1.64 TPSA 63.2 ✓ Ro5 ✓ Clean [O-][P-](=O)[O-]
SEP
4IJ6
D3DFG8 185.1 Da LogP -1.49 TPSA 130.1 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)OP(=O)(O)O
VO4
3GP5
Q3JWH7 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=O)([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.