Structure of PDB 9ja1 Chain A Binding Site BS06

Receptor Information

>9ja1 Chain A (length=1286) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSESRGGCGNTQPTIRKDGLKLVGSWLRVLSTEEILNIFKHISVKDFTSL
GFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKA
NISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPV
KSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK
TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAG
DIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNL
SVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG
IVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLW
SGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTV
GSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIAD
GPTMREITETIAEAKKKVLDVTKEAQALRESFEDNVVRFLNEARDKAGRL
AEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDR
TLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTA
ETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQS
LDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEE
YKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLT
IKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVL
QEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLN
TFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAK
LIRSAIEHTTLITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETD
GVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASD
GSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL
FEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI

Ligand information

Ligand ID

ATP

InChI

InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

ZKHQWZAMYRWXGA-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[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
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O

Formula

C10 H16 N5 O13 P3

Name

ADENOSINE-5'-TRIPHOSPHATE

PDB chain

9ja1 Chain T Residue 101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9ja1 The RNA polymerase II elongation complex from Saccharomyces cerevisiae
Resolution	2.98 Å
Binding residue (original residue number in PDB)	R446 P448 N479 L1081 F1084 H1085
Binding residue (residue number reindexed from 1)	R424 P426 N457 L1049 F1052 H1053
Annotation score	1

External links

PDB	RCSB:9ja1, PDBe:9ja1, PDBj:9ja1
PDBsum	9ja1
PubMed
UniProt	P04050\|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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