Protein profile

VK055_5141

putative L,D-transpeptidase ErfK/SrfK

Genome: KpATCC43816

Gene: AIK83664.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQE8
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Amino acids 300
Annotations 8
Features 12
PDB binders 0
Druggability 0.268

Overview

Basic information about this protein and its source genome.

Accession
VK055_5141
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83664.1
Status
annotated
Amino acids
300
Structure source
AlphaFold + ColabFold
GO
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. 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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor). GO:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
39.394
Localization
Unknown
ColabFold pLDDT
91.23

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 0.268
Structure A0A0H3GQE8
Pocket Pocket 5
P2Rank 0.663
Structure A0A0H3GQE8
Pocket Pocket 1
ColabFold model
FPocket 0.343 · Pocket 9
P2Rank 0.838 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 136 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • 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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
  • GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
  • GO:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 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:0018104 The process of covalently linking peptidoglycan (murein) to proteins.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
74 219 Gene3D G3DSA:2.40.440.10 -
74 219 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
3 228 PANTHER PTHR30582 L,D-TRANSPEPTIDASE
85 220 SUPERFAMILY SSF141523 L,D-transpeptidase catalytic domain-like
85 220 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
81 220 FunFam G3DSA:2.40.440.10:FF:000001 L,D-transpeptidase YbiS
87 217 CDD cd16913 YkuD_like
87 217 InterPro IPR005490 L,D-transpeptidase catalytic domain
223 291 Pfam PF17969 L,D-transpeptidase C-terminal domain
223 291 InterPro IPR041597 L,D-transpeptidase C-terminal domain
86 218 Pfam PF03734 L,D-transpeptidase catalytic domain
86 218 InterPro IPR005490 L,D-transpeptidase catalytic domain

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_A0A0H3GQE8
AlphaFold — — full sequence — Viewing
ColabFold VK055_5141
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
5 0.268
2 0.026
11 0.005
12 0.003

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 15.11 0.663
2 3.07 0.082
3 2.87 0.073