Structure of PDB 6cd1 Chain H Binding Site BS01

Receptor Information

>6cd1 Chain H (length=452) Species: 3880 (Medicago truncatula)

FLDYGLSEADPDVHAIINKEKDRQFRSLELIASENFTSKAVMEAVGSCLT
NKYSEGLPGKRYYGGNEHIDELEILCQQRALAAFHLDGDKWGVNVQPLSG
SPANFAVYTAILKPHDRIMGLDLPHGGHLSHGFMTAKRRVSGTSIYFESM
PYRLDESTGVIDYDMLEKTAALFRPKLIIAGASAYPRDIDYARFRKIADS
VGAFLMMDMAHVSGLIAASVLADPFEFVDIVTTTTHKSLRGPRGGMIFFK
KDAVHGVDLESAINNAVFPGLQGGPHNHTIGGLAVCLKYAQSPDFKNYQN
QVVANCRALANRLVEHEYKLVSGGSDNHLVLVDLRPSGIDGARVEKILDM
ASITLNKNSVPGDKSALVPGGIRIGSPAMTTRGLGEKEFELIADLIHEGV
RISLEAKSLVSGTKVQDFLNFVLAPEFPLGDKVSNLRRKVEALATQYPIP
GV

Ligand information

• Ligand ID: GLY
• InChI: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
• InChIKey: DHMQDGOQFOQNFH-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C(=O)O)N
  CACTVS 3.341: NCC(O)=O
  ACDLabs 10.04: O=C(O)CN
• Formula: C2 H5 N O2
• Name: GLYCINE
• ChEMBL: CHEMBL773
• DrugBank: DB00145
• ZINC: ZINC000004658552
• PDB chain: 6cd1 Chain H Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6cd1 Chloroplastic Serine Hydroxymethyltransferase FromMedicago truncatula: A Structural Characterization.
• Resolution: 1.91 Å
• Binding residue (original residue number in PDB): H292 X318 R454
• Binding residue (residue number reindexed from 1): H211 X237 R373
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): Y134 E136 D289 T315 K318 R324
• Catalytic site (residue number reindexed from 1): Y53 E55 D208 T234 K237 R243
• 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:6cd1, PDBe:6cd1, PDBj:6cd1
• PDBsum: 6cd1
• PubMed: 29868052
• UniProt: G7ILW0