Structure of PDB 1kmk Chain A Binding Site BS01

Receptor Information
>1kmk Chain A (length=405) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IFSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGY
AAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLV
ANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGT
LQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDG
AQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEG
GGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNN
IAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFL
DNYGIAVRTGHHCAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRI
HRLLG
Ligand information
Ligand IDSEC
InChIInChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
InChIKeyZKZBPNGNEQAJSX-REOHCLBHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(N)C[SeH]
OpenEye OEToolkits 1.7.6C(C(C(=O)O)N)[SeH]
OpenEye OEToolkits 1.7.6C([C@@H](C(=O)O)N)[SeH]
CACTVS 3.370N[C@@H](C[SeH])C(O)=O
CACTVS 3.370N[CH](C[SeH])C(O)=O
FormulaC3 H7 N O2 Se
NameSELENOCYSTEINE
ChEMBLCHEMBL109962
DrugBankDB02345
ZINC
PDB chain1kmk Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kmk Analysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H123 N175 K226 R359 X364 R379
Binding residue
(residue number reindexed from 1)		H122 N174 K225 R358 X363 R378
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) H123 D200 A202 Q203 K226 R359 C364
Catalytic site (residue number reindexed from 1) H122 D199 A201 Q202 K225 R358 C363
Enzyme Commision number 2.8.1.7: cysteine desulfurase.
3.13.1.-
4.4.1.16: selenocysteine lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008826 cysteine sulfinate desulfinase activity
GO:0009000 selenocysteine lyase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0031071 cysteine desulfurase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0001887 selenium compound metabolic process
GO:0006534 cysteine metabolic process
GO:0006790 sulfur compound metabolic process
GO:0016226 iron-sulfur cluster assembly
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1kmk, PDBe:1kmk, PDBj:1kmk
PDBsum1kmk
PubMed11827487
UniProtP77444|SUFS_ECOLI Cysteine desulfurase (Gene Name=sufS)

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