Structure of PDB 6qmm Chain B Binding Site BS02

Receptor Information
>6qmm Chain B (length=280) Species: 1140 (Synechococcus elongatus PCC 7942 = FACHB-805) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVWIDEVFEDRVRYGLRGQILWEETSPFQKITIVDTEHYGRGLLLDDCWM
TAERCEVCYHEYLVHPPLTTAASIARVLVIGGGDGGTVREVLRYAEVEQV
DLVEIDGRVVELSQEYLGAIGTAWADPRLNVKIGDGIAFVQTAPDASYDV
ILVDGSDPAGPAAGLFNREFYENCRRVLKPGGVFASQAESPDSFLAVHLE
MIETLSAVFAEAKPYYGWVPMYPSGWWSWLYASDTPGQFQKPQSDRLAAI
EPQVEIYNRDIHQAAFAQPNFVRRGLSARQ
Ligand information
Ligand IDMTA
InChIInChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyWUUGFSXJNOTRMR-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H15 N5 O3 S
Name5'-DEOXY-5'-METHYLTHIOADENOSINE
ChEMBLCHEMBL277041
DrugBankDB02282
ZINCZINC000004228245
PDB chain6qmm Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6qmm Crystal structure of dimericSynechococcusspermidine synthase with bound polyamine substrate and product.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		M55 G86 D89 E109 I110 G141 D159 P166 A167
Binding residue
(residue number reindexed from 1)		M50 G81 D84 E104 I105 G136 D154 P161 A162
Annotation score5
Enzymatic activity
Enzyme Commision number 2.5.1.16: spermidine synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0016740 transferase activity
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0008295 spermidine biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6qmm, PDBe:6qmm, PDBj:6qmm
PDBsum6qmm
PubMed30877192
UniProtQ31QK9|SPEE_SYNE7 Polyamine aminopropyltransferase (Gene Name=speE)

[Back to BioLiP]