Protein profile

KP13_04897

Peptidoglycan-binding lysin domain-containing protein

Genome: KpKP13

Gene: AHE45257.1 Structure source: AlphaFold + ColabFold UniProt A0A447S5P8
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Amino acids 281
Annotations 9
Features 23
PDB binders 0
Druggability 0.668

Overview

Basic information about this protein and its source genome.

Accession
KP13_04897
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45257.1
Status
annotated
Amino acids
281
Structure source
AlphaFold + ColabFold
EC
2.-.-.-
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)
Y
DEG identity (%)
41.379
DEG E-value
2.11e-63
Localization
Unknown
ColabFold pLDDT
94.41

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 0.668
Structure A0A447S5P8
Pocket Pocket 1
P2Rank 0.85
Structure A0A447S5P8
Pocket Pocket 1
ColabFold model
FPocket 0.42 · Pocket 4
P2Rank 0.841 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 126 / 4744 genomes with a hit
Normalized 0.027

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: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.

23 records
Show feature table
Start End DB Term Name
5 50 CDD cd00118 LysM
5 50 InterPro IPR018392 LysM domain
58 201 FunFam G3DSA:2.40.440.10:FF:000001 L,D-transpeptidase YbiS
6 51 Gene3D G3DSA:3.10.350.10 LysM domain
6 51 InterPro IPR036779 LysM domain superfamily
64 200 Pfam PF03734 L,D-transpeptidase catalytic domain
64 200 InterPro IPR005490 L,D-transpeptidase catalytic domain
6 51 SUPERFAMILY SSF54106 LysM domain
64 201 CDD cd16913 YkuD_like
64 201 InterPro IPR005490 L,D-transpeptidase catalytic domain
5 51 SMART SM00257 LysM_2
5 51 InterPro IPR018392 LysM domain
7 51 Pfam PF01476 LysM domain
7 51 InterPro IPR018392 LysM domain
5 50 ProSiteProfiles PS51782 LysM domain profile.
1 55 FunFam G3DSA:3.10.350.10:FF:000007 Probable L,D-transpeptidase YcfS
62 200 SUPERFAMILY SSF141523 L,D-transpeptidase catalytic domain-like
62 200 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
59 201 Gene3D G3DSA:2.40.440.10 -
59 201 InterPro IPR038063 L,D-transpeptidase catalytic domain-like
204 270 Pfam PF17969 L,D-transpeptidase C-terminal domain
204 270 InterPro IPR041597 L,D-transpeptidase C-terminal domain
4 209 PANTHER PTHR30582 L,D-TRANSPEPTIDASE

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_A0A447S5P8
AlphaFold — — full sequence — Viewing
ColabFold KP13_04897
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
1 0.668

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 16.81 0.788