Structure of PDB 8u9x Chain A Binding Site BS07

Receptor Information

>8u9x Chain A (length=1398) 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
LKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPE
VVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQY
GWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPY
NADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTL
CGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQIL
SVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGG
LIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMRE
ITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK
AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFG
FVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTA
VKTAEPGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHI
EKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVL
LDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKP
SDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLAT
RRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQ
MTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQ
EQAKLIRSAIEHTTLKSVTIASEIYYDPTVIPEDEEIIQLQQSPWLLRLE
LDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVEED
HMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLE
TDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIA
SDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVE
ILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMP

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

8u9x Chain B Residue 2501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	8u9x Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Resolution	3.05 Å
Binding residue (original residue number in PDB)	R446 P448 N479 F1084
Binding residue (residue number reindexed from 1)	R418 P420 N451 F1056
Annotation score	1

External links

PDB	RCSB:8u9x, PDBe:8u9x, PDBj:8u9x
PDBsum	8u9x
PubMed	39190355
UniProt	P04050\|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

[Back to BioLiP]