Structure of PDB 6rtd Chain B Binding Site BS02

Receptor Information
>6rtd Chain B (length=466) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APGEALYRQHCQACHGAGRLGGSGPTLLPESLSRLKPAQAREVILHGRPA
TQMAGFAGQLDDAAADALVAYLYQAPPREPQWSAEDIRASQVQPHPLATL
PSRPRFEADPLNLFVVVESGDHHVTILDGDRFEPIARFPSRYALHGGPKF
SPDGRLVYFASRDGWVTLYDLYNLKVVAEVRAGLNTRNLAVSDDGRWVLV
GNYLPGNLVLLDARDLSLVQVIPAADAQGQASRVSAVYTAPPRHSFVVAL
KDVHELWELPYANGKPVAPKRLAVADYLDDFSFSPDYRYLLGSSRQARGG
EVIELDSGARVASIPLSGMPHLGSGIYWKRDGRWVFATPNISRGVISVID
LQNWKPLKEIVTDGPGFFMRSHADSPYAWTDTFLGKKHDEILLIDKQTLE
IAHRLRPSPGKVAGHVEFTRDGRYALLSVWDRDGALVVYDAHSLEEVKRL
PMNKPSGKYNVGNKIG
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 B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		H147 G148 G149 K151 R164 R189 N190 H323 F369 F370 R372 H417 Y461
Binding residue
(residue number reindexed from 1)		H145 G146 G147 K149 R162 R187 N188 H321 F367 F368 R370 H415 Y459
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

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

[Back to BioLiP]