Protein profile

KP13_02520

Lipoprotein nlpD

Genome: KpKP13

Gene: AHE42984.1 nlpD Structure source: AlphaFold + ColabFold UniProt A0A0H3GWT3
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Amino acids 378
Annotations 5
Features 33
PDB binders 3
Druggability 0.005

Overview

Basic information about this protein and its source genome.

Accession
KP13_02520
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42984.1 nlpD
Status
annotated
Amino acids
378
Structure source
AlphaFold + ColabFold
GO
GO:0032153 The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles. GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. 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:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

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 (%)
0.0
Localization
OuterMembrane
ColabFold pLDDT
68.26

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 0.005
Structure A0A0H3GWT3
Pocket Pocket 10
P2Rank 0.301
Structure A0A0H3GWT3
Pocket Pocket 1
ColabFold model
FPocket 0.749 · Pocket 16
P2Rank 0.364 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 111 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0032153 The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • 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:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
1 12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
167 187 MobiDBLite mobidb-lite consensus disorder prediction
213 376 FunFam G3DSA:2.70.70.10:FF:000004 NlpD family lipoprotein
108 166 FunFam G3DSA:3.10.350.10:FF:000008 Murein hydrolase activator NlpD
114 157 Gene3D G3DSA:3.10.350.10 LysM domain
114 157 InterPro IPR036779 LysM domain superfamily
115 158 CDD cd00118 LysM
115 158 InterPro IPR018392 LysM domain
116 158 Pfam PF01476 LysM domain
116 158 InterPro IPR018392 LysM domain
39 378 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
278 371 Pfam PF01551 Peptidase family M23
278 371 InterPro IPR016047 Peptidase M23
115 375 SUPERFAMILY SSF51261 Duplicated hybrid motif
115 375 InterPro IPR011055 Duplicated hybrid motif
1 29 SignalP_EUK SignalP-noTM SignalP-noTM
115 159 SMART SM00257 LysM_2
115 159 InterPro IPR018392 LysM domain
13 26 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 38 Phobius SIGNAL_PEPTIDE Signal peptide region
35 86 MobiDBLite mobidb-lite consensus disorder prediction
1 26 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
278 362 CDD cd12797 M23_peptidase
107 375 PANTHER PTHR21666 PEPTIDASE-RELATED
219 376 Gene3D G3DSA:2.70.70.10 Glucose Permease (Domain IIA)
219 376 InterPro IPR011055 Duplicated hybrid motif
1 25 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
114 158 ProSiteProfiles PS51782 LysM domain profile.
114 158 InterPro IPR018392 LysM domain
27 38 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
63 86 MobiDBLite mobidb-lite consensus disorder prediction
35 55 MobiDBLite mobidb-lite consensus disorder prediction
1 24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM

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 + 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_A0A0H3GWT3
AlphaFold — — full sequence — Viewing
ColabFold KP13_02520
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 5.13 0.235
2 2.89 0.092
3 1.64 0.027

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.

22 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
4SQ
4ZYB
O33599 281.2 Da LogP -2.12 TPSA 158.8 ✓ Ro5 ✓ Clean C(CP(=O)(CNC(=O)CN)O)C(=O)NCC(=O)O
CAC
2B0P
O33599 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
TLA
2B13
O33599 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O

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.