Protein profile

PA4930

biosynthetic alanine racemase

Genome: NC_002516.2

Gene: PA4930 alr Structure source: Experimental + AlphaFold UniProt Q9HUN4
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Amino acids 358
Annotations 10
Features 42
PDB binders 7
Druggability 0.658

Overview

Basic information about this protein and its source genome.

Accession
PA4930
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4930 alr
Status
annotated
Amino acids
358
Structure source
Experimental + AlphaFold
EC
5.1.1.1
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008784 Catalysis of the reaction: L-alanine = D-alanine. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. GO:0030632 The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid. GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

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 0.658
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008784 Catalysis of the reaction: L-alanine = D-alanine.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0030632 The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008360 Any process that modulates the surface configuration of a cell.
  • 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:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
3 356 CDD cd06827 PLPDE_III_AR_proteobact
31 41 ProSitePatterns PS00395 Alanine racemase pyridoxal-phosphate attachment site.
31 41 InterPro IPR020622 Alanine racemase, pyridoxal-phosphate attachment site
213 358 FunFam G3DSA:2.40.37.10:FF:000002 Alanine racemase
233 357 SMART SM01005 Ala_racemase_C_2
233 357 InterPro IPR011079 Alanine racemase, C-terminal
8 234 SUPERFAMILY SSF51419 PLP-binding barrel
8 234 InterPro IPR029066 PLP-binding barrel
1 357 PANTHER PTHR30511 ALANINE RACEMASE
4 356 NCBIfam TIGR00492 alanine racemase
4 356 InterPro IPR000821 Alanine racemase
266 281 PRINTS PR00992 Alanine racemase signature
266 281 InterPro IPR000821 Alanine racemase
287 304 PRINTS PR00992 Alanine racemase signature
287 304 InterPro IPR000821 Alanine racemase
121 133 PRINTS PR00992 Alanine racemase signature
121 133 InterPro IPR000821 Alanine racemase
26 42 PRINTS PR00992 Alanine racemase signature
26 42 InterPro IPR000821 Alanine racemase
61 79 PRINTS PR00992 Alanine racemase signature
61 79 InterPro IPR000821 Alanine racemase
339 352 PRINTS PR00992 Alanine racemase signature
339 352 InterPro IPR000821 Alanine racemase
192 219 PRINTS PR00992 Alanine racemase signature
192 219 InterPro IPR000821 Alanine racemase
155 166 PRINTS PR00992 Alanine racemase signature
155 166 InterPro IPR000821 Alanine racemase
249 264 PRINTS PR00992 Alanine racemase signature
249 264 InterPro IPR000821 Alanine racemase
213 358 Gene3D G3DSA:2.40.37.10 Lyase, Ornithine Decarboxylase; Chain A, domain 1
213 358 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
8 219 Pfam PF01168 Alanine racemase, N-terminal domain
8 219 InterPro IPR001608 Alanine racemase, N-terminal
10 212 Gene3D G3DSA:3.20.20.10 Alanine racemase
10 212 InterPro IPR029066 PLP-binding barrel
227 357 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like
227 357 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
233 356 Pfam PF00842 Alanine racemase, C-terminal domain
233 356 InterPro IPR011079 Alanine racemase, C-terminal
10 215 FunFam G3DSA:3.20.20.10:FF:000002 Alanine racemase
3 357 Hamap MF_01201 Alanine racemase.
3 357 InterPro IPR000821 Alanine racemase

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

1 + 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 6A2F
X-ray 2.50 Å A,B
100.0% 1-358
PDBe RCSB PDBj File
Viewing
AlphaFold PA4930
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 0.658
2 0.559

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 6.51 0.329
2 5.51 0.263
3 4.65 0.202
4 3.47 0.126
5 2.56 0.073

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.

57 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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
MLI
6A2F 2.50 Å Open crystal
102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])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.