Structure of PDB 3dmi Chain A Binding Site BS01

Receptor Information

>3dmi Chain A (length=87) Species: 2850 (Phaeodactylum tricornutum)

GDVGAGEQIFNANCAACHAGGQNVIMPEKTLEKEALDQYLAGGRTEKSII
SQVTGGKNAMPAFGGRLSDEEIANVAAYVLASAEAGW

Ligand information

• Ligand ID: HEC
• 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,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
• InChIKey: HXQIYSLZKNYNMH-LJNAALQVSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
  OpenEye OEToolkits 1.5.0: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
  CACTVS 3.341: C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
  CACTVS 3.341: CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
• Formula: C34 H34 Fe N4 O4
• Name: HEME C
• PDB chain: 3dmi Chain A Residue 146

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dmi Crystallization and structural analysis of cytochrome c(6) from the diatom Phaeodactylum tricornutum at 1.5 A resolution.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): N58 C59 C62 H63 N68 I70 K74 T75 L76 A80 L81 Y84 Q97 V98 K102 N103 M105 F108
• Binding residue (residue number reindexed from 1): N13 C14 C17 H18 N23 I25 K29 T30 L31 A35 L36 Y39 Q52 V53 K57 N58 M60 F63
• 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:3dmi, PDBe:3dmi, PDBj:3dmi
• PDBsum: 3dmi
• PubMed: 19129656
• UniProt: Q8GTB5