Structure of PDB 8u9r Chain A Binding Site BS06

Receptor Information

>8u9r Chain A (length=1396) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PSRGCGNTQPTIRKDGLKLVGSWKELRVLSTEEILNIFKHISVKDFTSLG
FNEVFSRPEWMILTCLPVPPPPVRPSISFQRGEDDLTFKLADILKANISL
ETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSPVKSIRAR
LKGKEGRRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEV
VTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYG
WKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYN
ADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLC
GIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILS
VAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGL
IHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREI
TETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKA
GRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGF
VDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAV
KTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIE
KQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLL
DEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPS
DLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATR
RVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQM
TLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQE
QAKLIRSAIEHTTLKSVTIASEIYYDPTVIPEDEEIIQLQQSPWLLRLEL
DRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVEEDH
MLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLET
DGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIAS
DGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEI
LFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYM

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

8u9r Chain A Residue 1806 [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	8u9r Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Resolution	3.34 Å
Binding residue (original residue number in PDB)	R446 N479 D481 L1081 H1085
Binding residue (residue number reindexed from 1)	R417 N450 D452 L1052 H1056
Annotation score	1

External links

PDB	RCSB:8u9r, PDBe:8u9r, PDBj:8u9r
PDBsum	8u9r
PubMed	39190355
UniProt	P04050\|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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