Structure of PDB 8xmb Chain B Binding Site BS05

Receptor Information
>8xmb Chain B (length=1064) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLSELGEGFLQSFCKKAATSFFDKYGLISHQLNSYNYFIEHGLQNVFQSF
GEMLVEPSWRYATVKFGEVTVEKPTFFSDDKELEFLPWHARLQNMTYSAR
IKVNVQVEVFDILIGSIPVMVKSILCKTSEKGKENCKKGDCAFDQGGYFV
IKGAEKVFIAQEQMCTKRLWISNSPWTVSFRSENKRNRFIVRLSENEKAE
DYKRREKVLTVYFLSTEIPVWLLFFALGVSSDKEAMDLIAFDGDDASITN
SLIASIHVADAVCEAFRCGNNALTYVEQQIKSTKFPPAESVDECLHLYLF
PGLQSLKKKARFLGYMVKCLLNSYAGKRKCENRDSFRNKRIELAGELLER
EIRVHLAHARRKMTRAMQKHLSGKPIEHYLDASVITNGLSRAFSTGAWSH
PFRKMERVSGVVANLGRANPLQTLIDLRRTRQQVLYTGKVGDARYPHPSH
WGRVCFLSTPDGENCGLVKNMSLLGLVSTQSLESVVEKLFACGMEELMDD
TCTPLFGKHKVLLNGDWVGLCADSESFVAELKSRRRQSELPREMEIKRDK
DDNEVRIFTDAGRLLRPLLVVENLQKLKQEKPSQYPFDHLLDHGILELIG
IEEEEDCNTAWGIKQLLKEPKIYTHCELDLSFLLGVSCAVVPFANHDHGR
RVLYQSQKHCQQAIGFSSTNPNIRCDTLSQQLFYPQKPLFKTLASECLKK
EVLFNGQNAIVAVNVHLGYNQEDSIVMNKASLERGMFRSEQIRSYKAEVD
VQFGKTHDSLEDDGFPFIGANMSTGDIVIGRCHSIKLKHTERGIVQKVVL
SSNDEGKNFAAVSLRQVRSPCLGDKFSSMHGQKGVLGYLEEQQNFPFTIQ
GIVPDIVINPHAFPSRQTPGQLLEAALSKGIACPIQAYTKLTRHATPFST
PGVTEITEQLHRAGFSRWGNERVYNGRSGEMMRSMIFMGPTFYQRLVHMS
EDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGASANLHE
RLFTLSDSSQMHICRKCKTYANGPYCRVCVSSDHVVRVYVPYGAKLLCQE
LFSMGITLNFDTKL
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8xmb Chain Q Residue 101 [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]
PDB8xmb Transcription of the Plant RNA polymerase IV is prone to backtracking
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R714 K921 R954
Binding residue
(residue number reindexed from 1)		R651 K833 R866
Annotation score1
Gene Ontology
Molecular Function
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0030422 siRNA processing
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0050776 regulation of immune response
GO:0050832 defense response to fungus
GO:0080188 gene silencing by siRNA-directed DNA methylation
GO:0141007 siRNA-mediated retrotransposon silencing by heterochromatin formation
Cellular Component
GO:0000418 RNA polymerase IV complex
GO:0000419 RNA polymerase V complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0030880 RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8xmb, PDBe:8xmb, PDBj:8xmb
PDBsum8xmb
PubMed
UniProtQ9LK40|NRPD2_ARATH DNA-directed RNA polymerases IV and V subunit 2 (Gene Name=NRPD2)

[Back to BioLiP]