Structure of PDB 5gvm Chain A

Receptor sequence
>5gvmA (length=442) Species: 126793 (Plasmodium vivax Sal-1) [Search protein sequence]
MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRV
SNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLS
GSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFES
KLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDE
VNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFN
KKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQV
LLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAIN
VSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKI
TVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP
3D structure
PDB5gvm Antimalarial Inhibitors Targeting Serine Hydroxymethyltransferase (SHMT) with in Vivo Efficacy and Analysis of their Binding Mode Based on X-ray Cocrystal Structures
ChainA
Resolution2.24 Å
3D
structure
Catalytic site residues are labeled in the structure
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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 A S34 S100 G101 S102 H129 Y182 T183 D208 S210 H211 H236 K237 R371 S34 S100 G101 S102 H129 Y182 T183 D208 S210 H211 H236 K237 R371
BS02 G57 A L124 G128 H129 T183 K355 N356 T357 L124 G128 H129 T183 K355 N356 T357 MOAD: ic50=186nM
PDBbind-CN: -logKd/Ki=6.73,Kd=186nM
BS03 PLG A Y54 Y64 Y54 Y64
BS04 G57 A E56 Y63 E56 Y63 MOAD: ic50=186nM
PDBbind-CN: -logKd/Ki=6.73,Kd=186nM
Gene Ontology
Molecular Function
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
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:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5gvm, PDBe:5gvm, PDBj:5gvm
PDBsum5gvm
PubMed28537728
UniProtA5K8L9

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