Structure of PDB 6bxo Chain B Binding Site BS02

Receptor Information
>6bxo Chain B (length=320) Species: 1392998 (Candidatus Methanoperedens nitroreducens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFDFDLERILKTIKDKNCKKVGLQFPEGLKRQAINIAREIEEKTRANVII
SGNPCFGACDIDTILAGSVDILFHFGHAGMGEYENVVFIEARSNIDIIPA
VKTALNLLKANRIGLITTVQHVHKLEEACKVIKEYGKECVIGKGDPRAIY
PGQVLGCNFTAARVDCEEFIYIGSGIFHPLGVAIATKKRVIAADPFLNQA
VEVSPERFLRKRGGYIAKATGAKIFGIIVSTKSGQYRMKLAQKLKEIADK
HGKIGYIILMDLVTPEQLLAFKADAYVNTACPRITIDDAERFHAPVLTPQ
EFEIVLGERRWENMEMDEMI
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6bxo Chain B Residue 901 [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]
PDB6bxo Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Resolution1.655 Å
Binding residue
(original residue number in PDB)		F58 L157 G158 H180 K234 Q237 L264 V265 C283 R285 I286 D289
Binding residue
(residue number reindexed from 1)		F56 L155 G156 H178 K232 Q235 L262 V263 C281 R283 I284 D287
Annotation score3
Enzymatic activity
Enzyme Commision number 2.5.1.108: 2-(3-amino-3-carboxypropyl)histidine synthase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0090560 2-(3-amino-3-carboxypropyl)histidine synthase activity
Biological Process
GO:0017183 protein histidyl modification to diphthamide

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6bxo, PDBe:6bxo, PDBj:6bxo
PDBsum6bxo
PubMed29590073
UniProtA0A062UZ78

[Back to BioLiP]