Structure of PDB 4pcu Chain B Binding Site BS03

Receptor Information
>4pcu Chain B (length=489) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRI
NKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTI
IEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTP
TNARFDSPSSHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQ
QCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEE
LNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQE
GLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWML
QKGFLKEEDWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPV
VDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGR
LSHILEMDHFALVVHEQQRQMVFGVVTAIDLLNFVAAQE
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain4pcu Chain B Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4pcu Structural insight into the molecular mechanism of allosteric activation of human cystathionine beta-synthase by S-adenosylmethionine.
Resolution3.578 Å
Binding residue
(original residue number in PDB)		P422 L423 G442 F443 D444 Q445 V533 T535 I537 D538
Binding residue
(residue number reindexed from 1)		P374 L375 G394 F395 D396 Q397 V475 T477 I479 D480
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K119 S147 D281 S349
Catalytic site (residue number reindexed from 1) K77 S105 D239 S307
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pcu, PDBe:4pcu, PDBj:4pcu
PDBsum4pcu
PubMed25197074
UniProtP35520|CBS_HUMAN Cystathionine beta-synthase (Gene Name=CBS)

[Back to BioLiP]