Structure of PDB 4l28 Chain D Binding Site BS02

Receptor Information
>4l28 Chain D (length=493) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRI
NKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTI
IEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTP
TNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQ
QCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEE
LNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQE
GLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWML
QKGFLKEELEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFN
QAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTD
TLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQERD
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain4l28 Chain D Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4l28 Structural basis of regulation and oligomerization of human cystathionine beta-synthase, the central enzyme of transsulfuration.
Resolution2.626 Å
Binding residue
(original residue number in PDB)		R51 C52 T53 W54 R58 S63 P64 H65 A226 P229 L230 Y233 R266
Binding residue
(residue number reindexed from 1)		R9 C10 T11 W12 R16 S21 P22 H23 A184 P187 L188 Y191 R224
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K119 S147 D281 S285 L287 S349 P375
Catalytic site (residue number reindexed from 1) K77 S105 D239 S243 L245 S307 P333
Enzyme Commision number 4.2.1.22: cystathionine beta-synthase.
Gene Ontology
Molecular Function
GO:0004122 cystathionine beta-synthase activity
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0030170 pyridoxal phosphate binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050421 nitrite reductase (NO-forming) activity
GO:0070025 carbon monoxide binding
GO:0070026 nitric oxide binding
GO:0072341 modified amino acid binding
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0001958 endochondral ossification
GO:0001974 blood vessel remodeling
GO:0006534 cysteine metabolic process
GO:0006535 cysteine biosynthetic process from serine
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006801 superoxide metabolic process
GO:0009069 serine family amino acid metabolic process
GO:0010749 regulation of nitric oxide mediated signal transduction
GO:0019343 cysteine biosynthetic process via cystathionine
GO:0019344 cysteine biosynthetic process
GO:0019346 transsulfuration
GO:0019448 L-cysteine catabolic process
GO:0021587 cerebellum morphogenesis
GO:0031667 response to nutrient levels
GO:0042262 DNA protection
GO:0043066 negative regulation of apoptotic process
GO:0043418 homocysteine catabolic process
GO:0044272 sulfur compound biosynthetic process
GO:0050667 homocysteine metabolic process
GO:0051593 response to folic acid
GO:0060135 maternal process involved in female pregnancy
GO:0060351 cartilage development involved in endochondral bone morphogenesis
GO:0070814 hydrogen sulfide biosynthetic process
GO:0071456 cellular response to hypoxia
GO:0097746 blood vessel diameter maintenance
Cellular Component
GO:0005634 nucleus
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:4l28, PDBe:4l28, PDBj:4l28
PDBsum4l28
PubMed24043838
UniProtP35520|CBS_HUMAN Cystathionine beta-synthase (Gene Name=CBS)

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