Protein profile

KP13_00354

Methionine synthase

Genome: KpKP13

Gene: metH AHE46907.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKU6
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Amino acids 1227
Annotations 12
Features 56
PDB binders 8
Druggability 0.71

Overview

Basic information about this protein and its source genome.

Accession
KP13_00354
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
metH AHE46907.1
Status
annotated
Amino acids
1227
Structure source
AlphaFold + ColabFold
EC
2.1.1.13
GO
GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances. GO:0008270 Binding to a zinc ion (Zn). 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:0008705 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine. GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
57.447
Human E-value
5.62e-29
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.64

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 0.71
Structure A0A0H3GKU6
Pocket Pocket 1
P2Rank 0.968
Structure A0A0H3GKU6
Pocket Pocket 1
ColabFold model
FPocket 0.614 · Pocket 4
P2Rank 0.866 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 481 / 4744 genomes with a hit
Normalized 0.101

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:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
  • GO:0008270 Binding to a zinc ion (Zn).
  • 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:0008705 Catalysis of the reaction: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine.
  • GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

56 records
Show feature table
Start End DB Term Name
657 740 SMART SM01018 B12_binding_2_2
657 740 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
744 895 FunFam G3DSA:3.40.50.280:FF:000001 Methionine synthase
653 739 SUPERFAMILY SSF47644 Methionine synthase domain
653 739 InterPro IPR036594 Methionine synthase domain
938 1208 Pfam PF02965 Vitamin B12 dependent methionine synthase, activation domain
938 1208 InterPro IPR004223 Vitamin B12-dependent methionine synthase, activation domain
346 643 Gene3D G3DSA:3.20.20.20 -
346 643 InterPro IPR011005 Dihydropteroate synthase-like
660 733 Pfam PF02607 B12 binding domain
660 733 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
903 1226 SUPERFAMILY SSF56507 Methionine synthase activation domain-like
903 1226 InterPro IPR037010 Vitamin B12-dependent methionine synthase, activation domain superfamily
96 116 Coils Coil Coil
742 894 SUPERFAMILY SSF52242 Cobalamin (vitamin B12)-binding domain
742 894 InterPro IPR036724 Cobalamin-binding domain superfamily
360 598 Pfam PF00809 Pterin binding enzyme
360 598 InterPro IPR000489 Pterin-binding domain
905 1224 Gene3D G3DSA:3.10.196.10 -
905 1224 InterPro IPR037010 Vitamin B12-dependent methionine synthase, activation domain superfamily
356 630 SUPERFAMILY SSF51717 Dihydropteroate synthetase-like
356 630 InterPro IPR011005 Dihydropteroate synthase-like
897 1227 ProSiteProfiles PS50974 AdoMet activation domain profile.
897 1227 InterPro IPR004223 Vitamin B12-dependent methionine synthase, activation domain
346 642 FunFam G3DSA:3.20.20.20:FF:000002 Methionine synthase
646 740 FunFam G3DSA:1.10.1240.10:FF:000001 Methionine synthase
356 612 CDD cd00740 MeTr
644 740 Gene3D G3DSA:1.10.1240.10 Methionine synthase domain
644 740 InterPro IPR036594 Methionine synthase domain
744 895 Gene3D G3DSA:3.40.50.280 -
746 881 ProSiteProfiles PS51332 B12-binding domain profile.
746 881 InterPro IPR006158 Cobalamin (vitamin B12)-binding domain
748 840 Pfam PF02310 B12 binding domain
748 840 InterPro IPR006158 Cobalamin (vitamin B12)-binding domain
6 1224 PANTHER PTHR45833 METHIONINE SYNTHASE
1 1195 PIRSF PIRSF000381 Met_synth_MetH
1 1195 InterPro IPR011822 Cobalamin-dependent methionine synthase
659 871 CDD cd02069 methionine_synthase_B12_BD
659 871 InterPro IPR033706 Methionine synthase, B12-binding domain
936 1093 Gene3D G3DSA:1.10.288.10 -
2 338 FunFam G3DSA:3.20.20.330:FF:000001 Methionine synthase
1 340 Gene3D G3DSA:3.20.20.330 -
1 340 InterPro IPR036589 Homocysteine-binding domain superfamily
7 399 SUPERFAMILY SSF82282 Homocysteine S-methyltransferase
7 399 InterPro IPR036589 Homocysteine-binding domain superfamily
650 744 ProSiteProfiles PS51337 B12-binding N-terminal domain profile.
650 744 InterPro IPR003759 Cobalamin (vitamin B12)-binding module, cap domain
970 990 Coils Coil Coil
356 617 ProSiteProfiles PS50972 Pterin-binding domain profile.
356 617 InterPro IPR000489 Pterin-binding domain
17 325 Pfam PF02574 Homocysteine S-methyltransferase
17 325 InterPro IPR003726 Homocysteine-binding domain
12 1192 NCBIfam TIGR02082 methionine synthase
12 1192 InterPro IPR011822 Cobalamin-dependent methionine synthase
5 325 ProSiteProfiles PS50970 Homocysteine-binding domain profile.
5 325 InterPro IPR003726 Homocysteine-binding 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_A0A0H3GKU6
AlphaFold — — full sequence — Viewing
ColabFold KP13_00354
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 0.71

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 19.07 0.834
2 11.33 0.606
3 8.38 0.447
4 7.85 0.417
5 5.88 0.287

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.

58 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
B13
2I2X
Q46EH4 1321.3 Da LogP 1.51 TPSA 444.1 3 viol. ✓ Clean CC1=C2[C@@]([C@@H](C3=CC4C([C@@H](C5=C(C6[C@]([…
C2F
5VOO
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
1BMT
P13009 — — — Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O…
FLC
5VOP
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
1Q8A
Q9WYA5 135.2 Da LogP -0.28 TPSA 63.3 ✓ Ro5 ✓ Clean C(CS)[C@@H](C(=O)O)N
SFG
6BDY
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
4CCZ
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
3BOF
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.