Protein profile

PA1843

B12-dependent methionine synthase

Genome: NC_002516.2

Gene: PA1843 metH Structure source: AlphaFold UniProt Q9I2Q2
Amino acids 1234
Annotations 12
Features 54
PDB binders 7
Druggability 0.431

Overview

Basic information about this protein and its source genome.

Accession
PA1843
Gene
PA1843 metH
Status
annotated
Amino acids
1234
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
57.806
Human E-value
1.34e-83
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

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 0.431
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0008705 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0050667 The chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid. Homocysteine is an important intermediate in the metabolic reactions of its S-methyl derivative, methionine.
  • GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
  • GO:0046872 Binding to a metal ion.
  • GO:0042558 The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
  • GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
664 878 CDD cd02069 methionine_synthase_B12_BD
664 878 InterPro IPR033706 Methionine synthase, B12-binding domain
904 1234 ProSiteProfiles PS50974 AdoMet activation domain profile.
904 1234 InterPro IPR004223 Vitamin B12-dependent methionine synthase, activation domain
20 1200 NCBIfam TIGR02082 methionine synthase
20 1200 InterPro IPR011822 Cobalamin-dependent methionine synthase
367 605 Pfam PF00809 Pterin binding enzyme
367 605 InterPro IPR000489 Pterin-binding domain
664 737 Pfam PF02607 B12 binding domain
664 737 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
9 345 FunFam G3DSA:3.20.20.330:FF:000001 Methionine synthase
363 619 CDD cd00740 MeTr
750 902 FunFam G3DSA:3.40.50.280:FF:000001 Methionine synthase
651 745 Gene3D G3DSA:1.10.1240.10 Methionine synthase domain
651 745 InterPro IPR036594 Methionine synthase domain
750 902 Gene3D G3DSA:3.40.50.280 -
944 1101 Gene3D G3DSA:1.10.288.10 -
363 624 ProSiteProfiles PS50972 Pterin-binding domain profile.
363 624 InterPro IPR000489 Pterin-binding domain
24 332 Pfam PF02574 Homocysteine S-methyltransferase
24 332 InterPro IPR003726 Homocysteine-binding domain
912 1232 Gene3D G3DSA:3.10.196.10 -
912 1232 InterPro IPR037010 Vitamin B12-dependent methionine synthase, activation domain superfamily
945 1216 Pfam PF02965 Vitamin B12 dependent methionine synthase, activation domain
945 1216 InterPro IPR004223 Vitamin B12-dependent methionine synthase, activation domain
752 888 ProSiteProfiles PS51332 B12-binding domain profile.
752 888 InterPro IPR006158 Cobalamin (vitamin B12)-binding domain
909 1233 SUPERFAMILY SSF56507 Methionine synthase activation domain-like
909 1233 InterPro IPR037010 Vitamin B12-dependent methionine synthase, activation domain superfamily
9 345 Gene3D G3DSA:3.20.20.330 -
9 345 InterPro IPR036589 Homocysteine-binding domain superfamily
655 749 ProSiteProfiles PS51337 B12-binding N-terminal domain profile.
655 749 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
754 847 Pfam PF02310 B12 binding domain
754 847 InterPro IPR006158 Cobalamin (vitamin B12)-binding domain
657 744 SUPERFAMILY SSF47644 Methionine synthase domain
657 744 InterPro IPR036594 Methionine synthase domain
662 745 SMART SM01018 B12_binding_2_2
662 745 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
363 636 SUPERFAMILY SSF51717 Dihydropteroate synthetase-like
363 636 InterPro IPR011005 Dihydropteroate synthase-like
8 1203 PIRSF PIRSF000381 Met_synth_MetH
8 1203 InterPro IPR011822 Cobalamin-dependent methionine synthase
353 650 Gene3D G3DSA:3.20.20.20 -
353 650 InterPro IPR011005 Dihydropteroate synthase-like
748 900 SUPERFAMILY SSF52242 Cobalamin (vitamin B12)-binding domain
748 900 InterPro IPR036724 Cobalamin-binding domain superfamily
651 745 FunFam G3DSA:1.10.1240.10:FF:000001 Methionine synthase
12 332 ProSiteProfiles PS50970 Homocysteine-binding domain profile.
12 332 InterPro IPR003726 Homocysteine-binding domain
13 1232 PANTHER PTHR45833 METHIONINE SYNTHASE
15 406 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase
15 406 InterPro IPR036589 Homocysteine-binding domain superfamily
353 649 FunFam G3DSA:3.20.20.20:FF:000002 Methionine synthase

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1843
AlphaFold full sequence Viewing
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 0.431
5 0.396
3 0.247

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
C2F Q5SKM5 459.5 Da LogP -0.26 TPSA 202.8 1 viol. ✓ Clean C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…
COB P13009 Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O…
FLC Q5SKM5 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
HCS Q9WYA5 135.2 Da LogP -0.28 TPSA 63.3 ✓ Ro5 ✓ Clean C(CS)[C@@H](C(=O)O)N
SFG P13009 381.4 Da LogP -2.06 TPSA 208.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
THG Q99707 445.4 Da LogP -0.28 TPSA 211.6 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
YT3 Q9WYA5 88.9 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Y+3]

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.