Protein profile

KP13_05656

Peptide methionine sulfoxide reductase msrB

Genome: KpKP13

Gene: AHE45072.1 msrB Structure source: AlphaFold + ColabFold UniProt A0A0H3GVT9
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Amino acids 137
Annotations 7
Features 14
PDB binders 6
Druggability 0.544

Overview

Basic information about this protein and its source genome.

Accession
KP13_05656
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45072.1 msrB
Status
annotated
Amino acids
137
Structure source
AlphaFold + ColabFold
EC
1.8.4.12
GO
GO:0033743 Catalysis of the reaction: L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl-(R)-S-oxide-[protein] + [thioredoxin]-dithiol. GO:0016671 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide. GO:0030091 The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues. GO:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
56.25
Human E-value
1.2e-13
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
56.923
DEG E-value
1.3199999999999999e-48
Localization
Cytoplasmic
ColabFold pLDDT
95.22

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 0.544
Structure A0A0H3GVT9
Pocket Pocket 1
P2Rank 0.671
Structure A0A0H3GVT9
Pocket Pocket 1
ColabFold model
FPocket 0.41 · Pocket 7
P2Rank 0.668 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 268 / 4744 genomes with a hit
Normalized 0.056

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0033743 Catalysis of the reaction: L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl-(R)-S-oxide-[protein] + [thioredoxin]-dithiol.
  • GO:0016671 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
  • GO:0030091 The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
  • GO:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
7 129 ProSiteProfiles PS51790 Methionine-R-sulfoxide reductase (MsrB) domain profile.
7 129 InterPro IPR002579 Peptide methionine sulphoxide reductase MrsB domain
1 132 FunFam G3DSA:2.170.150.20:FF:000001 Peptide methionine sulfoxide reductase MsrB
1 136 Gene3D G3DSA:2.170.150.20 Peptide methionine sulfoxide reductase.
5 132 SUPERFAMILY SSF51316 Mss4-like
5 132 InterPro IPR011057 Mss4-like superfamily
9 127 Pfam PF01641 SelR domain
9 127 InterPro IPR002579 Peptide methionine sulphoxide reductase MrsB domain
4 133 PANTHER PTHR10173 METHIONINE SULFOXIDE REDUCTASE
4 133 InterPro IPR028427 Peptide methionine sulfoxide reductase MsrB
5 135 NCBIfam TIGR00357 peptide-methionine (R)-S-oxide reductase MsrB
5 135 InterPro IPR002579 Peptide methionine sulphoxide reductase MrsB domain
3 129 Hamap MF_01400 Peptide methionine sulfoxide reductase MsrB [msrB].
3 129 InterPro IPR002579 Peptide methionine sulphoxide reductase MrsB 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_A0A0H3GVT9
AlphaFold — — full sequence — Viewing
ColabFold KP13_05656
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 0.544
3 0.266
5 0.018
6 0.001

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 15.38 0.671
2 2.89 0.074
3 0.66 0.001

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.

56 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
CAC
1L1D
P14930 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
D1D
5FA9
Q73PT7 152.2 Da LogP 0.10 TPSA 40.5 ✓ Ro5 ✓ Clean C1[C@H]([C@@H](CSS1)O)O
DTT
5FA9
Q73PT7 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
MLI
3MAO
Q9NZV6 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
RSM
3HCI
Q8P4Q6 220.3 Da LogP -0.99 TPSA 75.3 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CC[S@](=O)C)C(=O)NC
SSM
3BQF
Q9JWM8 220.3 Da LogP -0.99 TPSA 75.3 ✓ Ro5 ✓ Clean CC(=O)N[C@@H](CC[S@@](=O)C)C(=O)NC

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.