Protein profile

VK055_4625

glyA

Genome: KpATCC43816

Gene: glyA AIK83159.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRS5
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Amino acids 417
Annotations 5
Features 20
PDB binders 12
Druggability 0.418

Overview

Basic information about this protein and its source genome.

Accession
VK055_4625
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
glyA AIK83159.1
Status
annotated
Amino acids
417
Structure source
AlphaFold + ColabFold
GO
GO:0019264 OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0004372 Catalysis of the reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine. GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
57.031
Human E-value
7.339999999999999e-42
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.602
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
98.38

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 0.418
Structure A0A0H3GRS5
Pocket Pocket 6
P2Rank 0.829
Structure A0A0H3GRS5
Pocket Pocket 1
ColabFold model
FPocket 0.454 · Pocket 7
P2Rank 0.735 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3140 / 4744 genomes with a hit
Normalized 0.662

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:0019264 OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004372 Catalysis of the reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine.
  • GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
37 280 Gene3D G3DSA:3.40.640.10 -
37 280 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
6 390 PANTHER PTHR11680 SERINE HYDROXYMETHYLTRANSFERASE
6 390 InterPro IPR001085 Serine hydroxymethyltransferase
6 416 SUPERFAMILY SSF53383 PLP-dependent transferases
6 416 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
270 416 FunFam G3DSA:3.90.1150.10:FF:000003 Serine hydroxymethyltransferase
1 417 PIRSF PIRSF000412 SHMT
1 417 InterPro IPR001085 Serine hydroxymethyltransferase
9 409 CDD cd00378 SHMT
9 409 InterPro IPR001085 Serine hydroxymethyltransferase
37 280 FunFam G3DSA:3.40.640.10:FF:000001 Serine hydroxymethyltransferase
9 386 Pfam PF00464 Serine hydroxymethyltransferase
9 386 InterPro IPR039429 Serine hydroxymethyltransferase-like domain
7 417 Hamap MF_00051 Serine hydroxymethyltransferase [glyA].
7 417 InterPro IPR001085 Serine hydroxymethyltransferase
11 416 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
11 416 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
221 237 ProSitePatterns PS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.
221 237 InterPro IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site

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_A0A0H3GRS5
AlphaFold — — full sequence — Viewing
ColabFold VK055_4625
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 0.111
4 0.022
5 0.016
2 0.0

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 22.57 0.829
2 2.46 0.055
3 1.39 0.014
4 0.65 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.

62 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
2BO
4WXG
Q5M0B4 350.3 Da LogP -0.37 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]([C@@H](C)O)C(…
ALO
2VMX
Q7SIB6 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](C(=O)O)N)O
CAC
4WXB
Q5M0B4 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DTH
6TI3
Q5M0B4 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@H](C(=O)O)N)O
EVM
6TGH
Q5M0B4 333.2 Da LogP -0.27 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C-](CO)C(=O)O)O
FFO
1DFO
P0A825 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
FON
1KL2
Q7SIB6 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…
MLI
6YMD
I7H6W6 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
O3Z
6TI4
Q5M4W1 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CO)C(=O)O)O
PLG
1DFO
P0A825 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PLS
6YMF
I7H6W6 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
PMP
6YMD
I7H6W6 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O

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.