Protein profile

VK055_2353

D-methionine ABC transporter, ATP-binding protein

Genome: KpATCC43816

Gene: metN AIK80950.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS83
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Amino acids 343
Annotations 6
Features 26
PDB binders 6
Druggability 0.434

Overview

Basic information about this protein and its source genome.

Accession
VK055_2353
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
metN AIK80950.1
Status
annotated
Amino acids
343
Structure source
AlphaFold + ColabFold
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0048473 The process in which D-methionine is transported across a lipid bilayer, from one side of a membrane to the other. GO:0033232 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + D-methionine(out/in) = ADP + phosphate + D-methionine(in/out). GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain. GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
67.647
Human E-value
1.01e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
46.154
DEG E-value
6.31e-11
Localization
CytoplasmicMembrane
ColabFold pLDDT
91.29

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 0.434
Structure A0A0H3GS83
Pocket Pocket 6
P2Rank 0.247
Structure A0A0H3GS83
Pocket Pocket 1
ColabFold model
FPocket 0.386 · Pocket 5
P2Rank 0.269 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 433 / 4744 genomes with a hit
Normalized 0.091

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0048473 The process in which D-methionine is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0033232 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + D-methionine(out/in) = ADP + phosphate + D-methionine(in/out).
  • GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
248 343 SUPERFAMILY SSF55021 ACT-like
248 343 InterPro IPR045865 ACT-like domain
2 242 PANTHER PTHR43166 AMINO ACID IMPORT ATP-BINDING PROTEIN
1 240 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 240 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 233 CDD cd03258 ABC_MetN_methionine_transporter
1 233 InterPro IPR041701 Methionine import ATP-binding protein MetN, ATP-binding domain
246 343 Gene3D G3DSA:3.30.70.260 -
265 340 SMART SM00930 NIL_2
265 340 InterPro IPR018449 NIL domain
1 232 FunFam G3DSA:3.40.50.300:FF:000233 Methionine import ATP-binding protein MetN
2 241 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
2 241 InterPro IPR003439 ABC transporter-like, ATP-binding domain
268 339 Pfam PF09383 NIL domain
268 339 InterPro IPR018449 NIL domain
30 217 SMART SM00382 AAA_5
30 217 InterPro IPR003593 AAA+ ATPase domain
141 155 ProSitePatterns PS00211 ABC transporters family signature.
141 155 InterPro IPR017871 ABC transporter-like, conserved site
246 343 FunFam G3DSA:3.30.70.260:FF:000014 Methionine import ATP-binding protein MetN
1 232 Gene3D G3DSA:3.40.50.300 -
1 232 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
21 169 Pfam PF00005 ABC transporter
21 169 InterPro IPR003439 ABC transporter-like, ATP-binding domain
1 343 NCBIfam TIGR02314 methionine ABC transporter ATP-binding protein MetN
1 343 InterPro IPR012692 ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria

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_A0A0H3GS83
AlphaFold — — full sequence — Viewing
ColabFold VK055_2353
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
6 0.434

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 3.24 0.112
2 2.94 0.094
3 2.68 0.079

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
2BA
7AHE
Q9KIF7 658.4 Da LogP -1.63 TPSA 309.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…
AGS
6CVL
P30750 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP
3C41
D0VWX4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AT4
5WS4
A0A0D8G707 443.3 Da LogP -0.81 TPSA 212.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BET
7AHH
Q9KIF7 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
LPP
7CHA
Q9HVW1 648.9 Da LogP 10.51 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)C…

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.