Structure of PDB 1m5r Chain B Binding Site BS04

Receptor Information
>1m5r Chain B (length=351) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKS
FDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTD
IRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKK
VDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMV
EFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQA
IAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYV
NNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAID
L
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain1m5r Chain B Residue 401 [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]
PDB1m5r A Base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition state analog
Resolution1.8 Å
Binding residue
(original residue number in PDB)		V18 G188 R191 R195 F213 G214 K237 I238 M240 V243 R269 E272
Binding residue
(residue number reindexed from 1)		V18 G188 R191 R195 F213 G214 K237 I238 M240 V243 R269 E272
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E22 F72 D100 R191
Catalytic site (residue number reindexed from 1) E22 F72 D100 R191
Enzyme Commision number 2.4.1.27: DNA beta-glucosyltransferase.
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0033821 DNA beta-glucosyltransferase activity
Biological Process
GO:0006304 DNA modification
GO:0019049 virus-mediated perturbation of host defense response
GO:0052170 symbiont-mediated suppression of host innate immune response
GO:0099018 symbiont-mediated evasion of host restriction-modification system

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1m5r, PDBe:1m5r, PDBj:1m5r
PDBsum1m5r
PubMed12445783
UniProtP04547|GSTB_BPT4 DNA beta-glucosyltransferase (Gene Name=bgt)

[Back to BioLiP]