Structure of PDB 6zn7 Chain B Binding Site BS02

Receptor Information

>6zn7 Chain B (length=411) Species: 264462 (Bdellovibrio bacteriovorus HD100)

TTNFDQEALLYHQQGKPGKIEVISSKPCATEKDLSLAYSPGVAAPCKAIA
KDPAKVYDYTAKGNLVAVISNGTAVLGLGNIGPAAGKPVMEGKGILFKQF
AGIDVFDIEVAATDVDVFCNAVRVLEPTFGGINLEDIKAPECFEIEERLK
KEMNIPVFHDDQHGTAIVSGAALLNACSITNRKMETVRIVVNGAGASANS
CAKIFIALGARRENIIMCDSQGVIYKGRTAGMNKYKEYFASETEARTLTE
ALRGADVFVGLSVAGALTPEMLKDMAKDPIIFAMANPEPEITPDKARAAR
PDAIIATGRSDYPNQVNNVLGFPSIFRGALDTRSTQINEEMKLAAVHALA
KLAREDVPDKVSATYGGKSFKFGRDYLIPKPFDTRVLLWVAPEVAKAAMK
SGVATRAIEDW

Ligand information

• Ligand ID: NAP
• InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 6zn7 Chain B Residue 802

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zn7 A rotary mechanism for allostery in bacterial hybrid malic enzymes.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): T179 N206 A208 G209 A210 S211 D233 S234 K250 L275 S276 M298 N300 V330
• Binding residue (residue number reindexed from 1): T165 N192 A194 G195 A196 S197 D219 S220 K236 L261 S262 M284 N286 V316
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y52 A88 K107 E149 D150 D174 D175 N300
• Catalytic site (residue number reindexed from 1): Y38 A74 K93 E135 D136 D160 D161 N286
• Enzyme Commision number: 1.1.1.40: malate dehydrogenase (oxaloacetate-decarboxylating) (NADP(+)).

Gene Ontology

Molecular Function

• 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:0051287 NAD binding

External links

• PDB: RCSB:6zn7, PDBe:6zn7, PDBj:6zn7
• PDBsum: 6zn7
• PubMed: 33623032
• UniProt: Q6MM14;
  Q6MM15