Structure of PDB 6rtd Chain A Binding Site BS01

Receptor Information
>6rtd Chain A (length=465) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGEALYRQHCQACHGAGRLGGSGPTLLPESLSRLKPAQAREVILHGRPAT
QMAGFAGQLDDAAADALVAYLYQAPPREPQWSAEDIRASQVQPHPLATLP
SRPRFEADPLNLFVVVESGDHHVTILDGDRFEPIARFPSRYALHGGPKFS
PDGRLVYFASRDGWVTLYDLYNLKVVAEVRAGLNTRNLAVSDDGRWVLVG
NYLPGNLVLLDARDLSLVQVIPAADAQGQASRVSAVYTAPPRHSFVVALK
DVHELWELPYANGKPVAPKRLAVADYLDDFSFSPDYRYLLGSSRQARGGE
VIELDSGARVASIPLSGMPHLGSGIYWKRDGRWVFATPNISRGVISVIDL
QNWKPLKEIVTDGPGFFMRSHADSPYAWTDTFLGKKHDEILLIDKQTLEI
AHRLRPSPGKVAGHVEFTRDGRYALLSVWDRDGALVVYDAHSLEEVKRLP
MNKPSGKYNVGNKIG
Ligand information
Ligand IDDHE
InChIInChI=1S/C34H34N4O10.Fe/c1-15-17(5-7-27(39)40)21-10-22-18(6-8-28(41)42)16(2)20(36-22)11-25-33(3,13-29(43)44)32(48)24(38-25)12-26-34(4,14-30(45)46)31(47)23(37-26)9-19(15)35-21;/h9-12H,5-8,13-14H2,1-4H3,(H6,35,36,37,38,39,40,41,42,43,44,45,46,47,48);/q;+2/p-2/t33-,34-;/m1./s1
InChIKeyXLQCGNUTSJTZNF-YDXXJHAFSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(C6=O)(C)CC(=O)O)C(=O)C(C8=C2)(C)CC(=O)O)C)CCC(=O)O
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7[C@@](C6=O)(C)CC(=O)O)C(=O)[C@](C8=C2)(C)CC(=O)O)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N@]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C@@](C)(CC(O)=O)C6=O)[C@@](C)(CC(O)=O)C5=O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C](C)(CC(O)=O)C6=O)[C](C)(CC(O)=O)C5=O
FormulaC34 H32 Fe N4 O10
NameHEME D
ChEMBL
DrugBank
ZINC
PDB chain6rtd Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rtd Crystal Structure of Dihydro-Heme d1Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		R36 H147 G148 G149 K151 R164 R189 H323 F369 F370 R372 Y461
Binding residue
(residue number reindexed from 1)		R33 H144 G145 G146 K148 R161 R186 H320 F366 F367 R369 Y458
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.-.-
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006783 heme biosynthetic process
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rtd, PDBe:6rtd, PDBj:6rtd
PDBsum6rtd
PubMed31173777
UniProtQ9I609|NIRN_PSEAE Dihydro-heme d1 dehydrogenase (Gene Name=nirN)

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