Structure of PDB 6ccz Chain A Binding Site BS03

Receptor Information

>6ccz Chain A (length=443) Species: 3880 (Medicago truncatula)

FLDYGLSEADPDVHAIINKEKDRQFRSLELIASENFTSKAVMEAVGSCLT
NKYSEGLPGKRYYGGNEHIDELEILCQQRALAAFHLDGDKWGVNVQPLSG
SPANFAVYTAILKPHDRIMGLDLPHGGHLSHGFRVSGTSIYFESMPYRLD
ESTGVIDYDMLEKTAALFRPKLIIAGASAYPRDIDYARFRKIADSVGAFL
MMDMAHVSGLIAASVLADPFEFVDIVTTTTHKSLRGPRGGMIFFKKDAVH
GVDLESAINNAVFPGLQGGPHNHTIGGLAVCLKYAQSPDFKNYQNQVVAN
CRALANRLVEHEYKLVSGGSDNHLVLVDLRPSGIDGARVEKILDMASITL
NKNSVPGDVPGGIRIGSPAMTTRGLGEKEFELIADLIHEGVRISLEAKSL
VSGTKVQDFLNFVLAPEFPLGDKVSNLRRKVEALATQYPIPGV

Ligand information

• Ligand ID: SEY
• InChI: InChI=1S/CH4N2Se/c2-1(3)4/h(H4,2,3,4)
• InChIKey: IYKVLICPFCEZOF-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.370: NC(N)=[Se]
  OpenEye OEToolkits 1.7.6: C(=[Se])(N)N
  ACDLabs 12.01: [Se]=C(N)N
• Formula: C H4 N2 Se
• Name: selenourea
• ChEMBL: CHEMBL3187603
• PDB chain: 6ccz Chain A Residue 605

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ccz Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
• Resolution: 2.14 Å
• Binding residue (original residue number in PDB): A263 Y266 V293
• Binding residue (residue number reindexed from 1): A177 Y180 V207
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y134 E136 D289 T315 K318 R324
• Catalytic site (residue number reindexed from 1): Y53 E55 D203 T229 K232 R238
• Enzyme Commision number: 2.1.2.1: glycine hydroxymethyltransferase.

Gene Ontology

Molecular Function

• GO:0004372 glycine hydroxymethyltransferase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0019264 glycine biosynthetic process from serine
• GO:0035999 tetrahydrofolate interconversion

External links

• PDB: RCSB:6ccz, PDBe:6ccz, PDBj:6ccz
• PDBsum: 6ccz
• PubMed: 29868052
• UniProt: G7ILW0