Structure of PDB 3d6c Chain A Binding Site BS02

Receptor Information

>3d6c Chain A (length=135) Species: 1280 (Staphylococcus aureus)

LHKEPATLIKAIDGDTVKLMYKGQPMTFRLLEVDTPETKHPKKGVEKYGP
EASAFTKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQ
GLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWS

Ligand information

• Ligand ID: THP
• InChI: InChI=1S/C10H16N2O11P2/c1-5-3-12(10(14)11-9(5)13)8-2-6(23-25(18,19)20)7(22-8)4-21-24(15,16)17/h3,6-8H,2,4H2,1H3,(H,11,13,14)(H2,15,16,17)(H2,18,19,20)/t6-,7+,8+/m0/s1
• InChIKey: CSNCBOPUCJOHLS-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(OP(=O)(O)O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)OP(=O)(O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O[P](O)(O)=O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)OP(=O)(O)O
• Formula: C10 H16 N2 O11 P2
• Name: THYMIDINE-3',5'-DIPHOSPHATE
• ChEMBL: CHEMBL1235491
• DrugBank: DB04205
• ZINC: ZINC000011422512
• PDB chain: 3d6c Chain A Residue 151

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d6c The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R35 D83 Y85 R87 L89 Y113 Y115
• Binding residue (residue number reindexed from 1): R29 D77 Y79 R81 L83 Y107 Y109
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D21 R35 D40 T41 E43 R87
• Catalytic site (residue number reindexed from 1): D15 R29 D34 T35 E37 R81
• Enzyme Commision number: 3.1.31.1: micrococcal nuclease.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004518 nuclease activity

External links

• PDB: RCSB:3d6c, PDBe:3d6c, PDBj:3d6c
• PDBsum: 3d6c
• PubMed: 19324049
• UniProt: P00644|NUC_STAAU Thermonuclease (Gene Name=nuc)