Structure of PDB 6bm4 Chain B Binding Site BS03

Receptor Information

>6bm4 Chain B (length=1097) Species: 559292 (Saccharomyces cerevisiae S288C)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATL
PYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFV
IQDRETALDFIGRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLG
YMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF
RYMQRTLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYS
STLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI
SVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPAR
LMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDES
LGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIA
MQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQ
SPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLK
FRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQE
KKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIG
KTTPITAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKI
PQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTV
AHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMY
NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS
RDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIA
KLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR

Ligand information

• Ligand ID: 2KH
• InChI: InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
• InChIKey: OZIBFYOFLVBDIY-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
  CACTVS 3.385: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.385: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
• Formula: C9 H16 N3 O14 P3
• Name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
• ZINC: ZINC000098208190
• PDB chain: 6bm4 Chain B Residue 1302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bm4 Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
• Resolution: 2.951 Å
• Binding residue (original residue number in PDB): R766 R1020
• Binding residue (residue number reindexed from 1): R653 R897
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D837
• Catalytic site (residue number reindexed from 1): D724
• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003729 mRNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II
• GO:0006367 transcription initiation at RNA polymerase II promoter
• GO:0006368 transcription elongation by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005665 RNA polymerase II, core complex
• GO:0005739 mitochondrion
• GO:0010494 cytoplasmic stress granule

External links

• PDB: RCSB:6bm4, PDBe:6bm4, PDBj:6bm4
• PDBsum: 6bm4
• PubMed: 29487211
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)