Structure of PDB 2dge Chain B Binding Site BS02

Receptor Information

>2dge Chain B (length=102) Species: 3702 (Arabidopsis thaliana)

QTLDIQRGATLFNRACIGCHDTGGNIIQPGATLFTKDLERNGVDTEEEIY
RVTYFGKGRMPGFGEKCTPRGQCTFGPRLQDEEIKLLAEFVKFQADQGWP
TV

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: 2dge Chain B Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dge Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): A85 C86 C89 H90 N95 I97 A101 T102 L103 D107 L108 N111 M130
• Binding residue (residue number reindexed from 1): A15 C16 C19 H20 N25 I27 A31 T32 L33 D37 L38 N41 M60
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0009055 electron transfer activity
• GO:0020037 heme binding

External links

• PDB: RCSB:2dge, PDBe:2dge, PDBj:2dge
• PDBsum: 2dge
• PubMed: 16777100
• UniProt: Q93VA3|CYC6_ARATH Cytochrome c6, chloroplastic (Gene Name=PETJ)