Protein profile

KP13_00750

50S ribosomal protein L4

Genome: KpKP13

Gene: rplD AHE42367.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU26
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Amino acids 201
Annotations 5
Features 13
PDB binders 7
Druggability 0.261

Overview

Basic information about this protein and its source genome.

Accession
KP13_00750
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rplD AHE42367.1
Status
annotated
Amino acids
201
Structure source
AlphaFold + ColabFold
GO
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:1990904 A macromolecular complex that contains both RNA and protein molecules. GO:0019843 Binding to a ribosomal RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
56.14
Human E-value
3.53e-14
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
99.005
DEG E-value
8.699999999999999e-147
Localization
Cytoplasmic
ColabFold pLDDT
95.43

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 0.261
Structure A0A0H3GU26
Pocket Pocket 2
P2Rank 0.007
Structure A0A0H3GU26
Pocket Pocket 1
ColabFold model
FPocket 0.292 · Pocket 4
P2Rank 0.014 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 240 / 4744 genomes with a hit
Normalized 0.051

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:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
  • GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
  • GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
  • GO:1990904 A macromolecular complex that contains both RNA and protein molecules.
  • GO:0019843 Binding to a ribosomal RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 201 Gene3D G3DSA:3.40.1370.10 -
1 201 InterPro IPR023574 Ribosomal protein L4 domain superfamily
10 200 PANTHER PTHR10746 50S RIBOSOMAL PROTEIN L4
10 200 InterPro IPR013005 50S ribosomal protein uL4
10 200 SUPERFAMILY SSF52166 Ribosomal protein L4
10 200 InterPro IPR023574 Ribosomal protein L4 domain superfamily
6 201 Hamap MF_01328_B 50S ribosomal protein L4 [rplD].
6 201 InterPro IPR013005 50S ribosomal protein uL4
1 201 FunFam G3DSA:3.40.1370.10:FF:000001 50S ribosomal protein L4
13 198 NCBIfam TIGR03953 50S ribosomal protein L4
13 198 InterPro IPR013005 50S ribosomal protein uL4
13 198 Pfam PF00573 Ribosomal protein L4/L1 family
13 198 InterPro IPR002136 Ribosomal protein L4/L1e

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

Loading 3D structure...

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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_A0A0H3GU26
AlphaFold — — full sequence — Viewing
ColabFold KP13_00750
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
2 0.261

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 1.54 0.023

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.

57 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
5MU
6O97
Q5SHN9 338.2 Da LogP -2.43 TPSA 171.3 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
FSD
6CZR
Q5SHN9 618.7 Da LogP -0.38 TPSA 210.7 3 viol. ✓ Clean C[C@@H]1[C@H](CC[C@@H](O1)N2C=CC(=NC2=O)NC(=O)c…
LUJ
6O97
Q5SHN9 641.7 Da LogP -6.81 TPSA 327.1 3 viol. ✓ Clean CCC[C@@H]1[C@H](O[C@@H]([C@@H]([C@H]1O)N)O[C@@H…
O
5LI0
Q2FW07 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
OHX
4V8E
Q5SHN9 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PSU
6O97
Q5SHN9 324.2 Da LogP -2.67 TPSA 182.2 1 viol. ✓ Clean C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2…
SPD
4WFA
Q2FW07 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN

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.