Structure of PDB 3hb3 Chain A Binding Site BS01

Receptor Information

>3hb3 Chain A (length=529) Species: 266 (Paracoccus denitrificans)

GFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMC
LEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFM
PLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVL
YPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFK
VPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVL
YQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIG
ILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGS
IEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVM
SLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFL
GRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKR
VNVPNYWNEHADTLEWTLPSPPPEHTFET

Ligand information

• Ligand ID: HEA
• InChI: InChI=1S/C49H58N4O6.Fe/c1-9-34-31(6)39-25-45-49(46(55)18-12-17-30(5)16-11-15-29(4)14-10-13-28(2)3)33(8)40(52-45)24-44-37(27-54)36(20-22-48(58)59)43(53-44)26-42-35(19-21-47(56)57)32(7)38(51-42)23-41(34)50-39;/h9,13,15,17,23-27,46,55H,1,10-12,14,16,18-22H2,2-8H3,(H4,50,51,52,53,54,56,57,58,59);/q;+2/p-2/b29-15+,30-17+,38-23-,39-25-,40-24-,41-23-,42-26-,43-26-,44-24-,45-25-;/t46-;/m0./s1
• InChIKey: ZGGYGTCPXNDTRV-PRYGPKJJSA-L
• SMILES:
  OpenEye OEToolkits 1.7.2: Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)[C@H](CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)O)C)CCC(=O)O)C
  CACTVS 3.370: CC(C)=CCC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
  CACTVS 3.370: CC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
  OpenEye OEToolkits 1.7.2: Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)C(CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)CCC(=O)O)C
  ACDLabs 12.01: O=C(O)CCC1=C(C2=Cc4c(c(c3C=C5C(=C(C=6C=C7C(C=O)=C(C8=CC1=N2[Fe](n34)(N5=6)N78)CCC(=O)O)C)C(O)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)C)C)/C=C)C
• Formula: C49 H56 Fe N4 O6
• Name: HEME-A
• PDB chain: 3hb3 Chain A Residue 559

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hb3 High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): T50 M53 R54 W87 I91 H94 M98 M99 V103 G163 W164 Y406 F412 H413 M416 S417 V421 I424 M452 I459 F460 R473 R474 F500
• Binding residue (residue number reindexed from 1): T34 M37 R38 W71 I75 H78 M82 M83 V87 G147 W148 Y390 F396 H397 M400 S401 V405 I408 M436 I443 F444 R457 R458 F484
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y35 I45 F49 M53 I91 H94 N113 D124 N131 S134 Y138 W164 S192 S193 G196 T203 H276 E278 Y280 S291 P307 H325 H326 T351 K354 H411 F412 H413 R473 R474
• Catalytic site (residue number reindexed from 1): Y19 I29 F33 M37 I75 H78 N97 D108 N115 S118 Y122 W148 S176 S177 G180 T187 H260 E262 Y264 S275 P291 H309 H310 T335 K338 H395 F396 H397 R457 R458
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006119 oxidative phosphorylation
• GO:0009060 aerobic respiration
• GO:0015990 electron transport coupled proton transport
• GO:0022904 respiratory electron transport chain
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0045277 respiratory chain complex IV

External links

• PDB: RCSB:3hb3, PDBe:3hb3, PDBj:3hb3
• PDBsum: 3hb3
• PubMed: 19374884
• UniProt: P98002|COX1B_PARDE Cytochrome c oxidase subunit 1-beta (Gene Name=ctaDII)