Structure of PDB 5xnh Chain H Binding Site BS02

Receptor Information

>5xnh Chain H (length=338) Species: 69014 (Thermococcus kodakarensis KOD1)

SHMREIIERVKEKTTIPVYERTIENVLSAIQASGDVWRIVDLSEEPLPLV
VAVVTALYELGYVAFENNQVILTRKGKELVEKYGIGPRADYTCSHCQGRT
VEIDAFSELLEQFKEITRDRPEPAHQFDQAYVTPETTVARVALMHSRGDL
ENKEVFVLGDDDLTSVALMLSGLPKRIAVLDIDERLTKFIEKAADEIGYE
NIEIFTRKPLPDYALHKFDTFITDPPETVEAIRAFVGRGIATLKGPGCAG
YFGITRRESSLDKWREIQRVLLNEFGVVITDIIRNFNEYVNWGYVEETRA
WRLLPIKVKPSYNWYKSYMFRIQTLEGSKGFDEESSTT

Ligand information

• Ligand ID: SPD
• InChI: InChI=1S/C7H19N3/c8-4-1-2-6-10-7-3-5-9/h10H,1-9H2
• InChIKey: ATHGHQPFGPMSJY-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(CCNCCCN)CN
  ACDLabs 10.04: NCCCNCCCCN
  CACTVS 3.341: NCCCCNCCCN
• Formula: C7 H19 N3
• Name: SPERMIDINE;
  N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;
  PA(34)
• ChEMBL: CHEMBL19612
• DrugBank: DB03566
• ZINC: ZINC000001532612
• PDB chain: 5xnh Chain H Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xnh Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): D126 D225 E228 G254 T256 Y290 Y316 T353
• Binding residue (residue number reindexed from 1): D128 D224 E227 G253 T255 Y289 Y315 T337
• Annotation score: 5

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