Structure of PDB 5mms Chain F Binding Site BS02

Receptor Information

>5mms Chain F (length=341) Species: 9606 (Homo sapiens)

IRPDALSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRIN
KIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTII
EPTSGNTGIGLALAAAVRGYRCIIVMPSSEKVDVLRALGAEIVRTSHVGV
AWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVG
TGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGI
GYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAV
AVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFL

Ligand information

• Ligand ID: HEM
• InChI: InChI=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-;
• InChIKey: KABFMIBPWCXCRK-RGGAHWMASA-L
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c2n3c(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 3.385: CC1=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 12.01: C=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
• Formula: C34 H32 Fe N4 O4
• Name: PROTOPORPHYRIN IX CONTAINING FE;
  HEME
• DrugBank: DB18267
• PDB chain: 5mms Chain F Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mms A Clinically Relevant Variant of the Human Hydrogen Sulfide-Synthesizing Enzyme Cystathionine beta-Synthase: Increased CO Reactivity as a Novel Molecular Mechanism of Pathogenicity?
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): S50 R51 C52 T53 W54 R58 S63 P64 H65 A226 P229 L230 Y233 R266
• Binding residue (residue number reindexed from 1): S7 R8 C9 T10 W11 R15 S20 P21 H22 A170 P173 L174 Y177 R210
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K119 S147 D281 S285 L287 S349 P375
• Catalytic site (residue number reindexed from 1): K76 S104 D225 S229 L231 S293 P319
• Enzyme Commision number: 4.2.1.22: cystathionine beta-synthase.

Gene Ontology

Molecular Function

• GO:0004122 cystathionine beta-synthase activity

Biological Process

• GO:0006535 cysteine biosynthetic process from serine
• GO:0019343 cysteine biosynthetic process via cystathionine

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5mms, PDBe:5mms, PDBj:5mms
• PDBsum: 5mms
• PubMed: 28421128
• UniProt: P35520|CBS_HUMAN Cystathionine beta-synthase (Gene Name=CBS)