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Structure of PDB 6vo6 Chain B Binding Site BS01

Receptor Information

>6vo6 Chain B (length=310) Species: 192222 (Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819)

SKKVLITGGAGYIGSVLTPILLEKGYEVCVIDNLMFDQISLLSCFHNKNF
TFINGDAMDENLIRQEVAKADIIIPLAALVGAPLCKRNPKLAKMINYEAV
KMISDFASPSQIFIYPNTNSGYGIGEKDAMCTEESPLRPISEYGIDKVHA
EQYLLDKGNCVTFRLATVFGISPRMRLDLLVNDFTYRAYRDKFIVLFEEH
FRRNYIHVRDVVKGFIHGIENYDKMKGQAYNMGLSSANLTKRQLAETIKK
YIPDFYIHSANIGEDPDKRDYLVSNTKLEATGWKPDNTLEDGIKELLRAF
KMMKVNRFAN

Ligand information

• Ligand ID: NAI
• InChI: InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BOPGDPNILDQYTO-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
• Formula: C21 H29 N7 O14 P2
• Name: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
  NADH
• ChEMBL: CHEMBL1234616
• DrugBank: DB00157
• ZINC: ZINC000008215403
• PDB chain: 6vo6 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vo6 Structural Analysis of Cj1427, an Essential NAD-Dependent Dehydrogenase for the Biosynthesis of the Heptose Residues in the Capsular Polysaccharides ofCampylobacter jejuni.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): G9 G12 Y13 I14 D33 N34 M36 Q39 D57 A58 L77 A78 V81 I96 P117 N118 Y144 K148 L166 V169 R175 R177
• Binding residue (residue number reindexed from 1): G8 G11 Y12 I13 D32 N33 M35 Q38 D56 A57 L76 A77 V80 I95 P116 N117 Y143 K147 L165 V168 R174 R176
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): T119 Y144 K148
• Catalytic site (residue number reindexed from 1): T118 Y143 K147
• Enzyme Commision number: 1.1.98.-

Gene Ontology

Molecular Function

• GO:0003978 UDP-glucose 4-epimerase activity
• GO:0016491 oxidoreductase activity
• GO:0019003 GDP binding
• GO:0042802 identical protein binding
• GO:0070404 NADH binding

Biological Process

• GO:0045227 capsule polysaccharide biosynthetic process
• GO:0051289 protein homotetramerization

External links

• PDB: RCSB:6vo6, PDBe:6vo6, PDBj:6vo6
• PDBsum: 6vo6
• PubMed: 32168450
• UniProt: Q0P8I7|GMHD_CAMJE GDP-D-glycero-alpha-D-manno-heptose dehydrogenase (Gene Name=Cj1427c)

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