Protein profile

KP13_03340

Rod shape-determining protein rodA

Genome: KpKP13

Gene: mrdB AHE45719.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLD1
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Amino acids 370
Annotations 10
Features 38
PDB binders 1
Druggability 0.951

Overview

Basic information about this protein and its source genome.

Accession
KP13_03340
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
mrdB AHE45719.1
Status
annotated
Amino acids
370
Structure source
AlphaFold + ColabFold
EC
2.4.99.28
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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. GO:0008360 Any process that modulates the surface configuration of a cell. 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0015648 Enables the directed movement of lipid-linked peptidoglycans into, out of or within a cell, or between cells.

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 (%)
95.946
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
85.09

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 0.951
Structure A0A0H3GLD1
Pocket Pocket 16
P2Rank 0.74
Structure A0A0H3GLD1
Pocket Pocket 1
ColabFold model
FPocket 0.955 · Pocket 20
P2Rank 0.605 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 193 / 4744 genomes with a hit
Normalized 0.041

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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.
  • GO:0008360 Any process that modulates the surface configuration of a cell.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015648 Enables the directed movement of lipid-linked peptidoglycans into, out of or within a cell, or between cells.
  • GO:0008955 Catalysis of the reaction: [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H+.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
96 135 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
333 337 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
50 68 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 99 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
181 203 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
50 67 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
290 309 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
69 73 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15 37 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 365 PANTHER PTHR30474 CELL CYCLE PROTEIN
7 365 InterPro IPR001182 Probable peptidoglycan glycosyltransferase FtsW/RodA
360 370 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
160 179 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
20 38 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
160 176 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
136 155 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
306 328 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
183 202 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
338 360 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
39 49 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
17 364 NCBIfam TIGR02210 rod shape-determining protein RodA
17 364 InterPro IPR011923 Probable peptidoglycan glycosyltransferase RodA/MrdB
177 182 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
321 345 ProSitePatterns PS00428 Cell cycle proteins ftsW / rodA / spoVE signature.
321 345 InterPro IPR018365 Cell cycle, FtsW / RodA / SpoVE, conserved site
74 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
310 332 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
136 154 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
338 359 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 366 Hamap MF_02079 Peptidoglycan glycosyltransferase MrdB [mrdB].
12 366 InterPro IPR011923 Probable peptidoglycan glycosyltransferase RodA/MrdB
203 262 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
272 294 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
20 364 Pfam PF01098 Cell cycle protein
20 364 InterPro IPR001182 Probable peptidoglycan glycosyltransferase FtsW/RodA
155 159 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
263 289 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GLD1
AlphaFold — — full sequence — Viewing
ColabFold KP13_03340
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
16 0.951
1 0.236

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 10.51 0.565
2 8.32 0.443
3 3.42 0.123
4 2.8 0.086
5 1.68 0.029

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.

51 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
OLC
6BAR
Q5SIX3 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.