Structure of PDB 5yg3 Chain B

Receptor sequence
>5yg3B (length=442) Species: 5855 (Plasmodium vivax) [Search protein sequence]
MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRV
SNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLS
GSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFES
KLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDE
VNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFN
KKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQV
LLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAIN
VSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKI
TVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP
3D structure
PDB5yg3 Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold
ChainB
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) Y54 E56 D208 T234 K237 R243
Catalytic site (residue number reindexed from 1) Y54 E56 D208 T234 K237 R243
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 PLG B Y54 Y64 Y54 Y64
BS02 8UC B E56 Y63 Y64 E56 Y63 Y64 PDBbind-CN: -logKd/Ki=7.85,IC50=0.014uM
BS03 PLG B S34 S100 G101 S102 H129 Y182 T183 D208 H211 H236 K237 R371 S34 S100 G101 S102 H129 Y182 T183 D208 H211 H236 K237 R371
BS04 8UC B L124 G128 H129 L130 T183 K355 C364 L124 G128 H129 L130 T183 K355 C364 PDBbind-CN: -logKd/Ki=7.85,IC50=0.014uM
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008168 methyltransferase activity
GO:0008270 zinc ion binding
GO:0030170 pyridoxal phosphate binding
GO:0050897 cobalt ion binding
GO:0070905 serine binding
Biological Process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0019264 glycine biosynthetic process from serine
GO:0032259 methylation
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yg3, PDBe:5yg3, PDBj:5yg3
PDBsum5yg3
PubMed29655285
UniProtA0A1G4H5I1

[Back to BioLiP]