Protein profile

VK055_1655

penicillin-binding protein 6

Genome: KpATCC43816

Gene: dacC2 AIK80275.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUM1
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Amino acids 400
Annotations 11
Features 29
PDB binders 14
Druggability 0.669

Overview

Basic information about this protein and its source genome.

Accession
VK055_1655
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
dacC2 AIK80275.1
Status
annotated
Amino acids
400
Structure source
AlphaFold + ColabFold
EC
3.4.16.4
GO
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:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. 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.

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 (%)
53.297
DEG E-value
4.86e-141
Localization
CytoplasmicMembrane
ColabFold pLDDT
91.91

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 0.669
Structure A0A0H3GUM1
Pocket Pocket 6
P2Rank 0.172
Structure A0A0H3GUM1
Pocket Pocket 1
ColabFold model
FPocket 0.499 · Pocket 11
P2Rank 0.182 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 147 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • 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:0042803 Binding to an identical protein to form a homodimer.
  • 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.

29 records
Show feature table
Start End DB Term Name
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 27 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
32 266 Pfam PF00768 D-alanyl-D-alanine carboxypeptidase
32 266 InterPro IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
1 27 Phobius SIGNAL_PEPTIDE Signal peptide region
285 376 Pfam PF07943 Penicillin-binding protein 5, C-terminal domain
285 376 InterPro IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal
23 27 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
285 376 SMART SM00936 PBP5_C_2
12 285 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
12 285 InterPro IPR012338 Beta-lactamase/transpeptidase-like
11 22 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
28 284 Gene3D G3DSA:3.40.710.10 -
28 284 InterPro IPR012338 Beta-lactamase/transpeptidase-like
151 164 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
151 164 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
65 76 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
65 76 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
124 141 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
124 141 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
36 289 PANTHER PTHR21581 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
285 378 SUPERFAMILY SSF69189 Penicillin-binding protein associated domain
285 378 InterPro IPR015956 Penicillin-binding protein, C-terminal domain superfamily
285 376 Gene3D G3DSA:2.60.410.10 -
285 376 InterPro IPR037167 D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily
285 376 FunFam G3DSA:2.60.410.10:FF:000001 D-alanyl-D-alanine carboxypeptidase dacA
28 400 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 27 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
22 284 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_A0A0H3GUM1
AlphaFold — — full sequence — Viewing
ColabFold VK055_1655
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
6 0.669
8 0.569
25 0.339
7 0.205

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 1.74 0.031

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
5TW4
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
3ITA
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
1Z6F
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
3HUM
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
3MZD
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
3BEC
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
3BEB
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
3MZF
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
6NTZ
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
5TY2
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
5J8X
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
5TX9
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
4K91
A0A0H2ZFH3 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
ZZ7
3HUN
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.