Structure of PDB 1ls3 Chain B Binding Site BS03

Receptor Information

>1ls3 Chain B (length=455) Species: 9986 (Oryctolagus cuniculus)

WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEA
LGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVN
VQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATS
IFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRL
RKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRA
GMIFYRRGVRSVDPYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMT
PEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRKGTDGGR
AEKVLEACSIACNKNTCPGKLRPSGLRLGTPALTSRGLLEKDFQKVAHFI
HRGIELTVQIQDDTGPRATLKEFKEDEKHQRAVRALRQEVESFAALFPLP
GLPGF

Ligand information

• Ligand ID: TGF
• InChI: InChI=1S/C30H37N9O13/c31-30-37-24-23(26(46)38-30)39(13-40)16(12-33-24)11-32-15-3-1-14(2-4-15)25(45)36-19(29(51)52)6-9-21(42)34-17(27(47)48)5-8-20(41)35-18(28(49)50)7-10-22(43)44/h1-4,13,16-19,32H,5-12H2,(H,34,42)(H,35,41)(H,36,45)(H,43,44)(H,47,48)(H,49,50)(H,51,52)(H4,31,33,37,38,46)/t16-,17-,18-,19-/m0/s1
• InChIKey: ZLOMJLIQXBKNHU-VJANTYMQSA-N
• SMILES:
  CACTVS 3.341: NC1=NC2=C(N(C=O)[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)CN2)C(=O)N1
  CACTVS 3.341: NC1=NC2=C(N(C=O)[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)C(O)=O)CN2)C(=O)N1
  ACDLabs 10.04: O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)NCC2N(C=3C(=O)NC(=NC=3NC2)N)C=O)CCC(=O)O
  OpenEye OEToolkits 1.5.0: c1cc(ccc1C(=O)NC(CCC(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)NC(=N3)N
  OpenEye OEToolkits 1.5.0: c1cc(ccc1C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O)NC[C@H]2CNC3=C(N2C=O)C(=O)NC(=N3)N
• Formula: C30 H37 N9 O13
• Name: 2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-4-CARBOXY-BUTYRYLAM INO)-4-CARBOXY-BUTYRYLAMINO]-PENTANEDIOIC ACID;
  TRIGLU-5-FORMYL-TETRAHYDROFOLATE
• ChEMBL: CHEMBL1236268
• DrugBank: DB02067
• ZINC: ZINC000055398661
• PDB chain: 1ls3 Chain B Residue 420C

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ls3 Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): G124 G125 H126 L127 K134A S175
• Binding residue (residue number reindexed from 1): G132 G133 H134 L135 K143 S189
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): Y55 E57 D200 T226 K229 R235
• Catalytic site (residue number reindexed from 1): Y59 E61 D214 T240 K243 R249
• Enzyme Commision number: 2.1.2.1: glycine hydroxymethyltransferase.

Gene Ontology

Molecular Function

• GO:0000900 mRNA regulatory element binding translation repressor activity
• GO:0004372 glycine hydroxymethyltransferase activity
• GO:0008270 zinc ion binding
• GO:0016740 transferase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0036094 small molecule binding
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0048027 mRNA 5'-UTR binding
• GO:0050897 cobalt ion binding
• GO:0070905 serine binding

Biological Process

• GO:0006544 glycine metabolic process
• GO:0006563 L-serine metabolic process
• GO:0006565 L-serine catabolic process
• GO:0006730 one-carbon metabolic process
• GO:0009113 purine nucleobase biosynthetic process
• GO:0017148 negative regulation of translation
• GO:0019264 glycine biosynthetic process from serine
• GO:0035999 tetrahydrofolate interconversion
• GO:0046653 tetrahydrofolate metabolic process
• GO:0046655 folic acid metabolic process
• GO:0051289 protein homotetramerization
• GO:1904482 cellular response to tetrahydrofolate
• GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1ls3, PDBe:1ls3, PDBj:1ls3
• PDBsum: 1ls3
• PubMed: 12438316
• UniProt: P07511|GLYC_RABIT Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)