Structure of PDB 8s5l Chain C Binding Site BS02

Receptor Information

>8s5l Chain C (length=507) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVR
INKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDT
IIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRT
PTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEIL
QQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPE
ELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQ
EGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWM
LQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREK
GFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIR
LTDTLGRLSHILEMDHFALVVHEQIQYHSTGKSSQRQMVFGVVTAIDLLN
FVAAQER

Ligand information

Ligand ID

PLP

InChI

InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)

InChIKey

NGVDGCNFYWLIFO-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0	Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04	O=P(O)(O)OCc1cnc(c(O)c1C=O)C

Formula

C8 H10 N O6 P

Name

PYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate

PDB chain

8s5l Chain C Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8s5l Architecture and regulation of filamentous human cystathionine beta-synthase.
Resolution	3.8 Å
Binding residue (original residue number in PDB)	K119 N149 G256 T257 G259 T260 S349 P375 D376
Binding residue (residue number reindexed from 1)	K78 N108 G215 T216 G218 T219 S308 P334 D335
Annotation score	1

Enzymatic activity

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

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Biological Process

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Cellular Component

External links

PDB	RCSB:8s5l, PDBe:8s5l, PDBj:8s5l
PDBsum	8s5l
PubMed	38575566
UniProt	P35520\|CBS_HUMAN Cystathionine beta-synthase (Gene Name=CBS)

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