Protein profile

VK055_5052

DD-carboxypeptidase, penicillin-binding protein 6b

Genome: KpATCC43816

Gene: AIK83578.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV65
Amino acids 347
Annotations 9
Features 21
PDB binders 14
Druggability 0.551

Overview

Basic information about this protein and its source genome.

Accession
VK055_5052
Gene
AIK83578.1
Status
annotated
Amino acids
347
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
46.356
DEG E-value
8.49e-111
Localization
CytoplasmicMembrane
ColabFold pLDDT
95.23

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 0.551
Structure A0A0H3GV65
Pocket Pocket 13
P2Rank 0.28
Structure A0A0H3GV65
Pocket Pocket 1
ColabFold model
FPocket 0.494 · Pocket 1
P2Rank 0.3 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 112 / 4744 genomes with a hit
Normalized 0.024

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:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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: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:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 240 Gene3D G3DSA:3.40.710.10 -
1 240 InterPro IPR012338 Beta-lactamase/transpeptidase-like
241 332 Pfam PF07943 Penicillin-binding protein 5, C-terminal domain
241 332 InterPro IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal
241 331 Gene3D G3DSA:2.60.410.10 -
241 331 InterPro IPR037167 D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily
241 332 SMART SM00936 PBP5_C_2
241 334 SUPERFAMILY SSF69189 Penicillin-binding protein associated domain
241 334 InterPro IPR015956 Penicillin-binding protein, C-terminal domain superfamily
1 221 Pfam PF00768 D-alanyl-D-alanine carboxypeptidase
1 221 InterPro IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
80 97 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
80 97 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
107 120 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
107 120 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
21 32 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
21 32 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
2 245 PANTHER PTHR21581 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
1 241 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
1 241 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 240 FunFam G3DSA:3.40.710.10:FF:000001 D-alanyl-D-alanine serine-type carboxypeptidase

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_A0A0H3GV65
AlphaFold full sequence Viewing
ColabFold VK055_5052
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
13 0.551

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 2.36 0.062

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.

65 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…
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.