Structure of PDB 6zng Chain D Binding Site BS02

Receptor Information
>6zng Chain D (length=750) Species: 264462 (Bdellovibrio bacteriovorus HD100) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNFDQEALLYHQQGKPGKIEVISSKPCATEKDLSLAYSPGVAAPCKAIAK
DPAKVYDYTAKGNLVAVISNGTAVLGLGNIGPAAGKPVMEGKGILFKQFA
GIDVFDIEVAATDVDVFCNAVRVLEPTFGGINLEDIKAPECFEIEERLKK
EMNIPVFHDDQHGTAIVSGAALLNACSITNRKMETVRIVVNGAGASANSC
AKIFIALGARRENIIMCDSQGVIYKGRTAGMNKYKEYFASETEARTLTEA
LRGADVFVGLSVAGALTPEMLKDMAKDPIIFAMANPEPEITPDKARAARP
DAIIATGRSDYPNQVNNVLGFPSIFRGALDTRSTQINEEMKLAAVHALAK
LAREDSFKFGRDYLIPKPFDTRVLLWVAPEVAKAAMKSGVATRAIEDWDQ
YRESLEALQGPSKVFIRSAINRVHQNSAANGGELPRIVFPEGTSTKVLKA
LATLVEEKICQPILLGYPERVKEKIKALDIPLLNDVSIVHPSSHPKYFSF
VEKLYSLRQRKGINLGEAERLMADPNYFAAMMVNQGEADGMVSGSSINYA
DAVRPILQTIGVYKEGIPAGLNFVLLEDKFLVLADTTVNLNPTAEQCAQI
ALQAAKIVEYFGIEPRVAMLSYSNFSGAEGTPRKMKKAAEIARSLRPDLM
IEGDMQADTAVNPEIMERLFPFSGLKGGANVLVFPNLESSNIAYKLIQQI
GKAEVIGPFLTGVRRSANVLQRTTTVDGIVNSVVFTALEAQYIKEVLKSR
Ligand information
Ligand IDACO
InChIInChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
InChIKeyZSLZBFCDCINBPY-ZSJPKINUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.341CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
CACTVS 3.341CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
FormulaC23 H38 N7 O17 P3 S
NameACETYL COENZYME *A
ChEMBLCHEMBL1230809
DrugBank
ZINCZINC000008551095
PDB chain6zng Chain D Residue 801 [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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PDB6zng A rotary mechanism for allostery in bacterial hybrid malic enzymes.
Resolution2.72 Å
Binding residue
(original residue number in PDB)		R535 K538 Y576 A577 R581 L584 P595 T614 V615 N616 L714 N718 K722
Binding residue
(residue number reindexed from 1)		R508 K511 Y549 A550 R554 L557 P568 T587 V588 N589 L687 N691 K695
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) Y52 A88 K107 E149 D150 D174 D175 N300
Catalytic site (residue number reindexed from 1) Y37 A73 K92 E134 D135 D159 D160 N285
Enzyme Commision number 1.1.1.40: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP(+)).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004470 malic enzyme activity
GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity
GO:0008948 oxaloacetate decarboxylase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016746 acyltransferase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006108 malate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6zng, PDBe:6zng, PDBj:6zng
PDBsum6zng
PubMed33623032
UniProtQ6MM14;
Q6MM15

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