Structure of PDB 8u8v Chain E Binding Site BS03

Receptor Information

>8u8v Chain E (length=990) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVML
GWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC
LEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVN
TSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHMELASRVCVVSVEK
PTLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRLEREVYEGRFSLYP
FLCLLDEREVVRMLLQVLQALPAQGESFTTLARELSARTFSRHVVQRQRV
SGQVQALQNHYRKYLCLLASDAEVPEPCLPRQYWEALGAPEALREQPWPL
PVQMELGKLLAEMLVQATQMPCSLDKPHRSSRLVPVLYHVYSFRNVQQIG
ILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTK
LMRTVEGATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQ
LFQAKGCPQLGVPAPPSEAPQPPEAHLPHSAAPARKAELRRELAHCQKVA
REMHSLRAEALYRLSLAQHLRDRVFWLPHNMDFRGRTYPCPPHFNHLGSD
VARALLEFAQGRPLGPHGLDWLKIHLVNLTGLKKREPLRKRLAFAEEVMD
DILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVRASDPAAYVSHLPV
HQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQ
DAQRGMRVAQVLEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSD
FPQEFVWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESARLISHMGSVVE
WVTPLGVPVIQPYRLDSRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHCY
RKGLTFVSVHDCYWTHAADVSVMNQVCREQFVRLHSEPILQDLSRFLVKR
FCSEPQKILEASQLKETLQAVPKPGAFDLEQVKRSTYFFS

Ligand information

Ligand ID

APC

InChI

InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1

InChIKey

CAWZRIXWFRFUQB-IOSLPCCCSA-N

SMILES

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

Formula

C11 H18 N5 O12 P3

Name

DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE

PDB chain

8u8v Chain E Residue 1301 [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	8u8v Structural basis for substrate binding and selection by human mitochondrial RNA polymerase.
Resolution	2.74 Å
Binding residue (original residue number in PDB)	S924 G927 R987 Q992 M995 Y999 H1125
Binding residue (residue number reindexed from 1)	S705 G708 R768 Q773 M776 Y780 H885
Annotation score	1

External links

PDB	RCSB:8u8v, PDBe:8u8v, PDBj:8u8v
PDBsum	8u8v
PubMed	39164235
UniProt	O00411\|RPOM_HUMAN DNA-directed RNA polymerase, mitochondrial (Gene Name=POLRMT)

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