Structure of PDB 5mfa Chain A Binding Site BS02

Receptor Information

>5mfa Chain A (length=588) Species: 9606 (Homo sapiens)

GCAYQDVGVTCPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDG
FSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWG
QLLDHDLDFTPEPAARASFVTGVNCETSCVQQPPCFPLKIPPNDPRIKNQ
ADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNM
SNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRS
SEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQI
ITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQ
PFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAK
LNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFC
GLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGR
VGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDN
TGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA

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: 5mfa Chain A Residue 812

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mfa Structure of human promyeloperoxidase (proMPO) and the role of the propeptide in processing and maturation.
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): M253 G256 Q257 D260 D264 F265 T266 E408 M409 T495 R499 G501 H502 F573 L583 R590
• Binding residue (residue number reindexed from 1): M97 G100 Q101 D104 D108 F109 T110 E252 M253 T339 R343 G345 H346 F417 L427 R434
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Q257 D260 H261 D262 T334 F336 D338 S340 R405 E408 H502
• Catalytic site (residue number reindexed from 1): Q101 D104 H105 D106 T178 F180 D182 S184 R249 E252 H346
• Enzyme Commision number: 1.11.2.2: myeloperoxidase.

Gene Ontology

Molecular Function

• GO:0003682 chromatin binding
• GO:0004601 peroxidase activity
• GO:0005515 protein binding
• GO:0008201 heparin binding
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0001878 response to yeast
• GO:0002149 hypochlorous acid biosynthetic process
• GO:0002679 respiratory burst involved in defense response
• GO:0006952 defense response
• GO:0006979 response to oxidative stress
• GO:0009612 response to mechanical stimulus
• GO:0019430 removal of superoxide radicals
• GO:0032094 response to food
• GO:0032496 response to lipopolysaccharide
• GO:0034374 low-density lipoprotein particle remodeling
• GO:0042742 defense response to bacterium
• GO:0042744 hydrogen peroxide catabolic process
• GO:0043066 negative regulation of apoptotic process
• GO:0050832 defense response to fungus
• GO:1990268 response to gold nanoparticle

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005764 lysosome
• GO:0030141 secretory granule
• GO:0035578 azurophil granule lumen
• GO:0042582 azurophil granule
• GO:0043231 intracellular membrane-bounded organelle
• GO:0070062 extracellular exosome
• GO:0097013 phagocytic vesicle lumen

External links

• PDB: RCSB:5mfa, PDBe:5mfa, PDBj:5mfa
• PDBsum: 5mfa
• PubMed: 28348079
• UniProt: P05164|PERM_HUMAN Myeloperoxidase (Gene Name=MPO)