Structure of PDB 1kl2 Chain A Binding Site BS03

Receptor Information
>1kl2 Chain A (length=405) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNK
YAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMA
VYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVI
DYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAH
IAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAI
FPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEG
FTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESP
FVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRV
AALTD
Ligand information
Ligand IDFON
InChIInChI=1S/C20H23N7O7/c21-20-25-16-15(18(32)26-20)27(9-28)12(8-23-16)7-22-11-3-1-10(2-4-11)17(31)24-13(19(33)34)5-6-14(29)30/h1-4,9,12-13,22H,5-8H2,(H,24,31)(H,29,30)(H,33,34)(H4,21,23,25,26,32)/t12-,13+/m1/s1
InChIKeyVVIAGPKUTFNRDU-OLZOCXBDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)C2=C(NC[CH](CNc3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O)N2C=O)N1
CACTVS 3.341NC1=NC(=O)C2=C(NC[C@@H](CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)N2C=O)N1
ACDLabs 10.04O=C(O)C(NC(=O)c1ccc(cc1)NCC3N(C2=C(NC(=NC2=O)N)NC3)C=O)CCC(=O)O
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2CNC3=C(N2C=O)C(=O)N=C(N3)N
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C=O)C(=O)N=C(N3)N
FormulaC20 H23 N7 O7
NameN-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid;
[6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE;
6R-FOLINIC ACID
ChEMBLCHEMBL1232801
DrugBankDB03256
ZINCZINC000009212428
PDB chain1kl2 Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kl2 Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G121 H122 S172 N341
Binding residue
(residue number reindexed from 1)		G121 H122 S172 N341
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Y51 E53 D197 T223 K226 R232
Catalytic site (residue number reindexed from 1) Y51 E53 D197 T223 K226 R232
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
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:0006545 glycine biosynthetic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0008652 amino acid biosynthetic 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
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kl2, PDBe:1kl2, PDBj:1kl2
PDBsum1kl2
PubMed11877399
UniProtQ7SIB6

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