Structure of PDB 4xd0 Chain A Binding Site BS03

Receptor Information
>4xd0 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 IDT3F
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-FQLHZTMTSA-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
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
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
FormulaC16 H27 N3 O14 P2
Name(3R,4S,5R,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-aminogalactose
ChEMBL
DrugBank
ZINCZINC000058638663
PDB chain4xd0 Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4xd0 New Role for the Ankyrin Repeat Revealed by a Study of the N-Formyltransferase from Providencia alcalifaciens.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
E75 F76 M104 Y105 S107 Y195 F218 Y221 Q222
Binding residue
(residue number reindexed from 1)
E75 F76 M104 Y105 S107 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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4xd0, PDBe:4xd0, PDBj:4xd0
PDBsum4xd0
PubMed25574689
UniProtF8RC03

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