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Structure of PDB 1j49 Chain B Binding Site BS01

Receptor Information

>1j49 Chain B (length=332) Species: 1585 (Lactobacillus delbrueckii subsp. bulgaricus)

MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGV
VVYQQLDYIAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVP
VYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVG
VVGTGHIGQVFMQIMEGFGAKVITYDIFRNPELEKKGYYVDSLDDLYKQA
DVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLD
SGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAF
YTTHAVRNMVVKAFDNNLELVEGKEAETPVKV

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  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)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)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)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]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)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 1j49 Chain B Residue 360

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1j49 Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Y102 I107 G155 H156 I157 Y175 D176 I177 V207 P208 N213 V234 S235 R236 H297 A299 F300
• Binding residue (residue number reindexed from 1): Y102 I107 G155 H156 I157 Y175 D176 I177 V207 P208 N213 V234 S235 R236 H297 A299 F300
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): S103 R236 D260 E265 H297
• Catalytic site (residue number reindexed from 1): S103 R236 D260 E265 H297
• Enzyme Commision number: 1.1.1.28: D-lactate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0008720 D-lactate dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
• 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:1j49, PDBe:1j49, PDBj:1j49
• PDBsum: 1j49
• PubMed: 12054772
• UniProt: P26297|LDHD_LACDA D-lactate dehydrogenase (Gene Name=ldhA)

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