Structure of PDB 5xnc Chain B Binding Site BS03

Receptor Information

>5xnc Chain B (length=354) Species: 69014 (Thermococcus kodakarensis KOD1)

GSHMREIIERVKEKTTIPVYERTIENVLSAIQASGDVWRIVDLSEEPLPL
VVAVVTALYELGYVAFENNQVILTRKGKELVEKYGIGPRADYTCSHCQGR
TVEIDAFSELLEQFKEITRDRPEPAHQFDQAYVTPETTVARVALMHSRGD
LENKEVFVLGDDDLTSVALMLSGLPKRIAVLDIDERLTKFIEKAADEIGY
ENIEIFTFDLRKPLPDYALHKFDTFITDPPETVEAIRAFVGRGIATLKGP
GCAGYFGITRRESSLDKWREIQRVLLNEFGVVITDIIRNFNEYVNWGYVE
ETRAWRLLPIKVKPSYNWYKSYMFRIQTLEGSKGFEDEITVGQELYDDEE
SSTT

Ligand information

• Ligand ID: N4P
• InChI: InChI=1S/C10H26N4/c11-5-1-2-8-14(9-3-6-12)10-4-7-13/h1-13H2
• InChIKey: CAARYRKDWMNHCB-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: C(CCN(CCCN)CCCN)CN
  CACTVS 3.385: NCCCCN(CCCN)CCCN
• Formula: C10 H26 N4
• Name: N,N-bis(3-aminopropyl)butane-1,4-diamine;
  N4-aminopropylspermidine
• PDB chain: 5xnc Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xnc Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
• Resolution: 1.84 Å
• Binding residue (original residue number in PDB): D126 A128 D159 D160 D225 P226 E228 G254 T256 Y290 Y295 Y316 T350
• Binding residue (residue number reindexed from 1): D129 A131 D162 D163 D228 P229 E231 G257 T259 Y293 Y298 Y319 T353
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.5.1.128: N(4)-bis(aminopropyl)spermidine synthase.

Gene Ontology

Molecular Function

• GO:0016740 transferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups

Biological Process

• GO:0006596 polyamine biosynthetic process
• GO:0009058 biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5xnc, PDBe:5xnc, PDBj:5xnc
• PDBsum: 5xnc
• PubMed: 28881427
• UniProt: Q5JIZ3|BPSA_THEKO N(4)-bis(aminopropyl)spermidine synthase (Gene Name=bpsA)