Structure of PDB 5xnc Chain D

Receptor sequence

>5xncD (length=353) Species: 69014 (Thermococcus kodakarensis KOD1)

SHMREIIERVKEKTTIPVYERTIENVLSAIQASGDVWRIVDLSEEPLPLV
VAVVTALYELGYVAFENNQVILTRKGKELVEKYGIGPRADYTCSHCQGRT
VEIDAFSELLEQFKEITRDRPEPAHQFDQAYVTPETTVARVALMHSRGDL
ENKEVFVLGDDDLTSVALMLSGLPKRIAVLDIDERLTKFIEKAADEIGYE
NIEIFTFDLRKPLPDYALHKFDTFITDPPETVEAIRAFVGRGIATLKGPG
CAGYFGITRRESSLDKWREIQRVLLNEFGVVITDIIRNFNEYVNWGYVEE
TRAWRLLPIKVKPSYNWYKSYMFRIQTLEGSKGFEDEITVGQELYDDEES
STT

3D structure

• PDB: 5xnc Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
• Chain: D
• Resolution: 1.84 Å

Enzymatic activity

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

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FE	D	C91 C94	C93 C96
BS02	MTA	D	F125 D126 Q127 D159 D179 I180 F205 D206 L207 P227 F236 Y343	F127 D128 Q129 D161 D181 I182 F207 D208 L209 P229 F238 Y345
BS03	N4P	D	D126 A128 D159 D160 D225 P226 E228 G254 Y290 Y295 Y316 T350	D128 A130 D161 D162 D227 P228 E230 G256 Y292 Y297 Y318 T352

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)