Structure of PDB 4xcz Chain A Binding Site BS02

Receptor Information
>4xcz Chain A (length=397) Species: 126385 (Providencia alcalifaciens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLIIAGKNNIAVDVTKWIIKTISDIELYSVCNENDHGNDSFQLSFKKFC
IQFNIPIISLEDAYHLEDAIFLSLEFDKIIHPSKFTHNRIFNIHFSYLPA
YKGMYTSAWPILNNEQESGVTLHKIDHGIDTGAIIDQQKFPLDIEETAKT
LYLKYIKIGTEIVIKNLPALISGNYSIVEQSAIKSSYYSKKSIDYKNLMI
DLNKTAHEILQQIRAFTFRDYQLPRIDDIDIFHGEILSSKSLSKPGTILE
KNNYHLILSTIDYDIKLYSDNFDEILTACEDKSPEFISKLLKTENILFEK
NHLGWSPIIIAAYHGNMDVIEWLVSKGVNINDRNYKGTTVAMYFKDYMLR
SGNYTGLENLINLGLDLFLKDNEGLSVFDYMRKNKNIELFNFMSTFN
Ligand information
Ligand IDT3Q
InChIInChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12-,13-,15-/m1/s1
InChIKeyKVYJLJOGNUNRJK-HALQBZCBSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](N)[CH]1O
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O
CACTVS 3.341C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](N)[C@@H]1O
FormulaC16 H27 N3 O14 P2
Name[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate;
thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose
ChEMBL
DrugBank
ZINCZINC000008436920
PDB chain4xcz Chain A Residue 402 [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]
PDB4xcz New Role for the Ankyrin Repeat Revealed by a Study of the N-Formyltransferase from Providencia alcalifaciens.
Resolution1.5 Å
Binding residue
(original residue number in PDB)
E75 F76 G103 M104 Y105 S107 Y152 Y195 F218 Y221 Q222
Binding residue
(residue number reindexed from 1)
E75 F76 G103 M104 Y105 S107 Y152 Y195 F218 Y221 Q222
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.2.9: methionyl-tRNA formyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004479 methionyl-tRNA formyltransferase activity
Biological Process
GO:0006413 translational initiation
GO:0009058 biosynthetic process
GO:0071951 conversion of methionyl-tRNA to N-formyl-methionyl-tRNA
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4xcz, PDBe:4xcz, PDBj:4xcz
PDBsum4xcz
PubMed25574689
UniProtF8RC03

[Back to BioLiP]