Structure of PDB 3ddr Chain B Binding Site BS01

Receptor Information
>3ddr Chain B (length=753) Species: 615 (Serratia marcescens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDWVYDEPRSVSVISREQMDNRPARHAADILEQTTGAYSSVSQQDPALSV
NIRGIQDYGRVNMNIDGMRQNFQKSGHGQRNGTMYIDSELLSGVTIDKGT
TGGMGSAGTLGGIATFNTVSASDFLAPGKELGGKLHASTGDNGTHFIGSG
ILALGNETGDILLAASERHLGDYWPGNKGDIGNIRINNDTGNYDRYAESI
KNNKIPDTHYRMHSRLAKVGWNLPANQRLQLSYLQTQTASPIAGTLTNLG
TRPPYELGWKRTGYTDVMARNAAFDYSLAPEDVDWLDFQAKLYYVDTQDD
SDTYSTSSLLDNGYATRTRLRTYGAQAQNTSRFSLAPGHDFRANYGLEFY
YDKATSDSSRQGMEGVTPAGNRSVASLFANLTYDYDGWLTLEGGLRYDRY
RLRGQTGLSYPDLAKDGQRYTIDNPCKALRLTGCSTTTREDWDVDRDQGK
LSPTLAVAVRPGVEWLELYTTYGKSWRPPAITETLTNGSAHSSSTQYPNP
FLQPERSRAWEVGFNVQQPDLWFEGDRLVAKVAYFDTKVDNYINLAIDRN
KPGLVQPSGGNAAYVNNLSKTRFRGLEYQLNYDAGVFYADLTYTHMIGKN
EFCSNKAWLGGRLRYGDGSRRGNFYVEPDAASNDFVTCDGGTQFGSAAYL
PGDRGSVTLGGRAFDRKLDAGVTVRFAPGYQDSSVPSNYPYLADWPKYTL
FDLYASYKLTDSLTLRGSVENLTNRAYVVSYGETLANTLGRGRTVQGGVE
YRF
Ligand information
Ligand IDHEM
InChIInChI=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-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(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 3.385CC1=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 12.01C=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
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain3ddr Chain D Residue 200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3ddr Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H603 S605 G671 G672
Binding residue
(residue number reindexed from 1)		H491 S493 G559 G560
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0015232 heme transmembrane transporter activity
GO:0015344 siderophore uptake transmembrane transporter activity
GO:0022857 transmembrane transporter activity
GO:0046872 metal ion binding
Biological Process
GO:0015886 heme transport
GO:0033214 siderophore-dependent iron import into cell
GO:0044718 siderophore transmembrane transport
GO:0055085 transmembrane transport
Cellular Component
GO:0009279 cell outer membrane
GO:0019867 outer membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3ddr, PDBe:3ddr, PDBj:3ddr
PDBsum3ddr
PubMed19144921
UniProtQ79AD2

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