Protein profile

PA3999

D-ala-D-ala-carboxypeptidase

Genome: NC_002516.2

Gene: GNQ48_15470 ALP65_01315 GUL26_00120 dacC dacA CAZ10_26335 L4V69_08330 PAERUG_P19_London_7_VIM_2_05_10_06697 PA3999 Structure source: AlphaFold UniProt Q9X6V7 UniProt G3XD74
Amino acids 386
Annotations 9
Features 28
PDB binders 15
Druggability 0.371

Overview

Basic information about this protein and its source genome.

Accession
PA3999
Gene
GNQ48_15470 ALP65_01315 GUL26_00120 dacC dacA CAZ10_26335 L4V69_08330 PAERUG_P19_London_7_VIM_2_05_10_06697 PA3999
Status
annotated
Amino acids
386
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

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

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 0.371
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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: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:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0008360 Any process that modulates the surface configuration of a cell.
  • GO:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
20 275 FunFam G3DSA:3.40.710.10:FF:000001 D-alanyl-D-alanine serine-type carboxypeptidase
276 366 Pfam PF07943 Penicillin-binding protein 5, C-terminal domain
276 366 InterPro IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal
1 24 SignalP_EUK SignalP-noTM SignalP-noTM
19 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
276 366 SMART SM00936 PBP5_C_2
276 366 Gene3D G3DSA:2.60.410.10 -
276 366 InterPro IPR037167 D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily
32 283 PANTHER PTHR21581 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
143 156 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
143 156 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
116 133 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
116 133 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
63 74 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
63 74 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
1 24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
25 386 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
24 275 Gene3D G3DSA:3.40.710.10 -
24 275 InterPro IPR012338 Beta-lactamase/transpeptidase-like
29 256 Pfam PF00768 D-alanyl-D-alanine carboxypeptidase
29 256 InterPro IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
10 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
8 276 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
8 276 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
276 368 SUPERFAMILY SSF69189 Penicillin-binding protein associated domain
276 368 InterPro IPR015956 Penicillin-binding protein, C-terminal domain superfamily

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

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3999
AlphaFold full sequence Viewing
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
5 0.365
7 0.264

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.

66 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
AI8 A0A0H2WY27 607.7 Da LogP 1.24 TPSA 185.7 2 viol. ✓ Clean CCON=C(c1nc(sn1)N)C(=O)N[C@H](C=O)[C@@H]2NC(=C(…
AIC P08506 349.4 Da LogP 0.32 TPSA 112.7 ✓ Ro5 ✓ Clean CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](…
BO9 P0AEB2 580.4 Da LogP 0.84 TPSA 212.6 2 viol. ✓ Clean B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(…
CEW A0A0H2WY27 401.5 Da LogP -0.89 TPSA 155.1 ✓ Ro5 ✓ Clean CC1=C(N[C@H](SC1)[C@@H](C=O)NC(=O)C(=NOC)C2=CSC…
CXV P0AEB2 437.9 Da LogP 2.50 TPSA 121.5 ✓ Ro5 ✓ Clean Cc1c(c(no1)c2ccccc2Cl)C(=O)N[C@@H](C=O)[C@@H]3N…
HJ2 P0AEB2 389.4 Da LogP -0.45 TPSA 179.0 1 viol. ✓ Clean CC1=C(N[C@H](SC1)[C@@H](C(=O)O)NC(=O)CCCC[C@@H]…
HJ3 P0AEB2 375.4 Da LogP -0.46 TPSA 158.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)CCCC[C@@H…
IM2 P0AEB2 301.4 Da LogP -0.23 TPSA 122.5 ✓ Ro5 ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…
MER O53380 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
MXR P0AEB2 385.5 Da LogP -0.35 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…
NFF A0A0H2WY27 416.5 Da LogP 2.43 TPSA 104.7 ✓ Ro5 ✓ Clean CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](…
OK3 P0AEB2 357.2 Da LogP 0.04 TPSA 142.1 ✓ Ro5 ✓ Clean [B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3…
RB6 A0A0H2WY27 536.6 Da LogP -1.50 TPSA 212.2 3 viol. ✓ Clean C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H]…
SIN A0A0H2ZFH3 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
ZZ7 A0A0H2WY27 367.4 Da LogP 0.15 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H]…

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.