Protein profile

PA2939

aminopeptidase

Genome: NC_002516.2

Gene: lap PA2939 Structure source: Experimental + AlphaFold UniProt Q9HZQ8
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Amino acids 536
Annotations 8
Features 23
PDB binders 6
Druggability 0.83

Overview

Basic information about this protein and its source genome.

Accession
PA2939
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
lap PA2939
Status
annotated
Amino acids
536
Structure source
Experimental + AlphaFold
EC
3.4.11.1
GO
GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. GO:0004177 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain. GO:0046872 Binding to a metal ion. GO:0008235 Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways. GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.897
Human E-value
4.8e-06
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Extracellular

Selected Druggability evidence

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 0.83
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005576 The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
  • GO:0004177 Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain.
  • GO:0046872 Binding to a metal ion.
  • GO:0008235 Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
  • GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
  • GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
243 499 Gene3D G3DSA:3.40.630.10 Zn peptidases
61 131 Gene3D G3DSA:3.40.630.10 Zn peptidases
1 31 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
143 268 CDD cd00538 PA
277 489 Pfam PF04389 Peptidase family M28
277 489 InterPro IPR007484 Peptidase M28
117 239 SUPERFAMILY SSF52025 PA domain
117 239 InterPro IPR046450 PA domain superfamily
1 29 SignalP_EUK SignalP-noTM SignalP-noTM
22 29 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 29 Phobius SIGNAL_PEPTIDE Signal peptide region
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
61 500 CDD cd03876 M28_SGAP_like
61 500 InterPro IPR041756 Peptidase M28, SGAP-like
1 24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
30 536 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
70 495 SUPERFAMILY SSF53187 Zn-dependent exopeptidases
155 253 Pfam PF02225 PA domain
155 253 InterPro IPR003137 PA domain
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
75 495 PANTHER PTHR12147 METALLOPEPTIDASE M28 FAMILY MEMBER
75 495 InterPro IPR045175 Peptidase M28 family
132 242 Gene3D G3DSA:3.50.30.30 -

3D Structure

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

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Structural evidence

5 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 8AC7
X-ray 1.40 Å A,B
95.1% 27-536
PDBe RCSB PDBj File
Viewing
PDB 8ACK
X-ray 1.78 Å A,B
95.1% 27-536
PDBe RCSB PDBj File
Loaded
PDB 8ACR
X-ray 2.10 Å A
95.1% 27-536
PDBe RCSB PDBj File
Loaded
PDB 8AC9
X-ray 2.35 Å A,B
91.4% 27-516
PDBe RCSB PDBj File
Loaded
PDB 8ACG
X-ray 2.84 Å A,B,C,D,E,F
91.4% 27-516
PDBe RCSB PDBj File
Loaded
AlphaFold PA2939
AlphaFold — — 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 0.355

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 20.93 0.864
2 15.02 0.742
3 10.68 0.573
4 3.07 0.102
5 2.54 0.071

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.

108 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
BES
2EK9
A2V759 308.4 Da LogP 0.53 TPSA 112.7 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc…
DPN
1TKH
P80561 165.2 Da LogP 0.64 TPSA 63.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](C(=O)O)N
DTR
1TKF
P80561 204.2 Da LogP 1.12 TPSA 79.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@H](C(=O)O)N
IOY
1XBU
P80561 291.1 Da LogP 1.25 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@H](C(=O)O)N)I
MED
1TKJ
P80561 149.2 Da LogP 0.15 TPSA 63.3 ✓ Ro5 ✓ Clean CSCC[C@H](C(=O)O)N
PHI
1TF9
P80561 291.1 Da LogP 1.25 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@@H](C(=O)O)N)I

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.