Structure of PDB 4b40 Chain B Binding Site BS01

Receptor Information

>4b40 Chain B (length=673) Species: 85995 (Mycothermus thermophilus)

PLAAYEVDDSTGYLTSDVGGPIQDQTSLKAGIRGPTLLEDFMFRQKIQHF
DHERVPERAVHARGAGAHGTFTSYADWSNITAASFLNATGKQTPVFVRFS
TAAGSRGSADTARDVHGFATRFYTDEGNFDIVGNNIPVFFIQDAIQFPDL
IHSVKPRPDNEIPQAATAHDSAWDFFSQQPSTMHTLFWAMSGHGIPRSYR
HMDGFGVHTFRFVKDDGSSKLIKWHFKSRQGKASLVWEEAQVLSGKNADF
HRQDLWDAIESGNGPEWDVCVQIVDESQAQAFGFDLLDPTKIIPEEYAPL
TKLGLLKLDRNPTNYFAETEQVMFQPGHIVRGIDFTEDPLLQGRLFSYLD
TQLNRNGGPNFEQLPINMPRVPIHNNNRDGAGQMFIHRNKYPYTPNTLNS
GYPRQANQNAGRGFFTAPGRTASGALVREVSPTFNDHWSQPRLFFNSLTP
VEQQFLVNAMRFEISLVKSEEVKKNVLTQLNRVSHDVAVRVAAAIGLGAP
DADDTYYHNNKTAGVSIVGSGPLPTIKTLRVGILATTSESSALDQAAQLR
TRLEKDGLVVTVVAETLREGVDQTYSTADATGFDGVVVVDGAAALFSSPL
FPTGRPLQIFVDAYRWGKPVGVCGGKSSEVLDAADVPEDGDGVYSEESVD
MFVEEFEKGLATFRFTDRFALDS

Ligand information

• Ligand ID: HDD
• InChI: InChI=1S/C34H32N4O5.Fe/c1-7-20-17(3)23-13-24-19(5)22(9-10-31(39)40)28(37-24)16-30-34(12-11-32(41)43-34)33(6,42)29(38-30)15-27-21(8-2)18(4)25(36-27)14-26(20)35-23;/h7-8,13-16,42H,1-2,9-12H2,3-6H3,(H,39,40);/q-4;+4/b23-13-,26-14-,29-15-,30-16-;/t33-,34+;/m0./s1
• InChIKey: UMGOPAWIGKFTRK-QQDQPIDJSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C6=Cc7c(c(c8n7[Fe]3(N64)N9C(=C2)C(=C(C9=C8)C=C)C)C)C=C)(C)O
  CACTVS 3.341: Cc1c(CCC(O)=O)c2C=C3N4C(=Cc5n6c(C=C7N8C(=Cc1n2[Fe]468)C(=C7C=C)C)c(C)c5C=C)[C](C)(O)[C]39CCC(=O)O9
  CACTVS 3.341: Cc1c(CCC(O)=O)c2C=C3N4C(=Cc5n6c(C=C7N8C(=Cc1n2[Fe@]468)C(=C7C=C)C)c(C)c5C=C)[C@](C)(O)[C@@]39CCC(=O)O9
  ACDLabs 10.04: O=C(O)CCc1c(c2C=C7C(=C(\C=C)C6=Cc5c(c(\C=C)c4C=C9N3C(=Cc1n2[Fe]3(n45)N67)C8(OC(=O)CC8)C9(O)C)C)C)C
  OpenEye OEToolkits 1.5.0: Cc1c2n3c(c1CCC(=O)O)C=C4C5(CCC(=O)O5)C(C6=Cc7c(c(c8n7[Fe]3(N64)N9C(=C2)C(=C(C9=C8)C=C)C)C)C=C)(C)O
• Formula: C34 H32 Fe N4 O5
• Name: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE;
  HEME
• PDB chain: 4b40 Chain B Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4b40 Investigating the Active Centre of the Scytalidium Thermophilum Catalase
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): R79 V81 H82 R119 V153 G154 N155 F160 F168 V228 H229 F345 L361 R365 S368 Y369 T372
• Binding residue (residue number reindexed from 1): R58 V60 H61 R98 V132 G133 N134 F139 F147 V207 H208 F324 L340 R344 S347 Y348 T351
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H82 N155 Q346
• Catalytic site (residue number reindexed from 1): H61 N134 Q325
• Enzyme Commision number: 1.11.1.6: catalase.

Gene Ontology

Molecular Function

• GO:0004096 catalase activity
• GO:0004601 peroxidase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006979 response to oxidative stress
• GO:0042744 hydrogen peroxide catabolic process
• GO:0098869 cellular oxidant detoxification

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4b40, PDBe:4b40, PDBj:4b40
• PDBsum: 4b40
• PubMed: 23545640
• UniProt: R4GRT8