Structure of PDB 6kd7 Chain A Binding Site BS01

Receptor Information

>6kd7 Chain A (length=327) Species: 592029 (Nonlabens dokdonensis DSW-6)

MNTLKSLRTTFLEELKSKVTATEPAGLYDPVHYILDLGGKRLRPLLTLMS
AEMYGATAKDAMNAAIAVEVFHNFTLLHDDIMDAADLRRGKETVHKKWDV
NTGILTGDAMLIMAYRLFEDYDKDKFYQLNKVFSRTALEVCEGQQHDVDF
ETRDDVSVPEYLNMIKLKTSVLVGCALQMGAIIAGVDEKEQELIYDYGIN
LGLAFQLMDDYLDAFGDPETFGKEVGGDIRENKKTYLYLKSIENNDCATE
LKEWFALHFENMTEEQIDEKKETVKVFFEQSGGAKATLDAIESYTQKALK
NIEELSIAPESKKQLTDFSLQLMGRKS

Ligand information

• Ligand ID: PPV
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)O
  CACTVS 3.341: O[P](O)(=O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: OP(=O)(O)OP(=O)(O)O
• Formula: H4 O7 P2
• Name: PYROPHOSPHATE
• ChEMBL: CHEMBL1160571
• DrugBank: DB04160
• ZINC: ZINC000006827695
• PDB chain: 6kd7 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kd7 Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R43 H72
• Binding residue (residue number reindexed from 1): R43 H72
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): K40 F74 D79 D83 R88 D147 K168 F205 D209 D210
• Catalytic site (residue number reindexed from 1): K40 F74 D79 D83 R88 D147 K168 F205 D209 D210

Gene Ontology

Molecular Function

• GO:0004659 prenyltransferase activity
• GO:0016740 transferase activity

Biological Process

• GO:0008299 isoprenoid biosynthetic process

External links

• PDB: RCSB:6kd7, PDBe:6kd7, PDBj:6kd7
• PDBsum: 6kd7
• PubMed: 31427080
• UniProt: L7W5I6