Structure of PDB 6cmz Chain C Binding Site BS02

Receptor Information

>6cmz Chain C (length=462) Species: 216591 (Burkholderia cenocepacia J2315)

KNEHTTLLVIGGGPGGYVAAIRAGQLGIPTVLVERDRLGGTCLNIGCIPS
KALIHVADAFEQACGHAGEGALGIRVRAPEIDIAKSVAWKDGIVDRLTRG
VGALLKKSGVRVLHGEARVIDGKTVEVVSAGHAVRIGCEHLLLATGSEPV
ELPSMPFGGHVVSSTDALSPATLPKRLVVVGAGYIGLELGIVYRKLGVDV
SVVEAAERVLPAYDAELVRPVADSLARLGVRLWLGHKVLGLDKHGAVRVQ
AADGAEQTLPADRVLVAVGRRPRVDGFGLETLMLDRNGRALRIDDTCRTS
MRNVWAIGDVAGEPMLAHRAMAQGEMVAELIAGRRRQFMPAAIPAVCFTD
PEIVTAGWSPDDAHAAGVDCLSASFPFAANGRAMTLQATDGFVRVVARRD
NHLIVGWQAVGRGVSELAAAFSQSLEMGARLEDIGGTIHAHPTLGEALQE
AALRALGHALHV

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 6cmz Chain C Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6cmz 2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): G182 E205 A206 K238 V239 V269
• Binding residue (residue number reindexed from 1): G181 E204 A205 K237 V238 V268
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): C43 C48 S51 Y185 E189 H442 E447
• Catalytic site (residue number reindexed from 1): C42 C47 S50 Y184 E188 H441 E446
• Enzyme Commision number: 1.8.1.4: dihydrolipoyl dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004148 dihydrolipoyl dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
• GO:0050660 flavin adenine dinucleotide binding

External links

• PDB: RCSB:6cmz, PDBe:6cmz, PDBj:6cmz
• PDBsum: 6cmz
• UniProt: B4EEF2