Structure of PDB 3d3z Chain A Binding Site BS01

Receptor Information

>3d3z Chain A (length=238) Species: 5061 (Aspergillus niger)

TIDTCSSDSPLSCQTDNEASCCFNSPGGSLLQTQFWDYDPSDGPSDSWTI
HGLWPDNCDGTYQEYCDESREYSNITSILEAQNRTELLSYMKEYWPDYEG
ADEDESFWEHEWNKHGTCINTIEPSCYTDYYAQEEVGDFFQQVVDLFKTL
DSYTALSDAGITPSEDATYKLSDIEDALAAIHDGYPPYVGCEDGALSQLY
YYFNVKGSAIGGTYVASERLEDSNCKDSGIKYPPKYSS

Ligand information

• Ligand ID: D3Z
• InChI: InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6+,7-,8-/m0/s1
• InChIKey: WUBAOANSQGKRHF-UCVXFZOQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC1C(C(C(O1)N2C=CC(=O)NC2=O)O)O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)C
  CACTVS 3.341: C[C@@H]1O[C@@H]([C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=O
  CACTVS 3.341: C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@@H]([C@H](O1)N2C=CC(=O)NC2=O)O)O
• Formula: C9 H12 N2 O5
• Name: 1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione
• PDB chain: 3d3z Chain A Residue 252

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d3z Crystal structue of Actibind a T2 RNase
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F35 H51 D97 Y98 F107
• Binding residue (residue number reindexed from 1): F35 H51 D97 Y98 F107
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H51 W54 Y62 E111 K114 H115
• Catalytic site (residue number reindexed from 1): H51 W54 Y62 E111 K114 H115
• Enzyme Commision number: 4.6.1.19: ribonuclease T2.

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0033897 ribonuclease T2 activity

Biological Process

• GO:0006401 RNA catabolic process

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:3d3z, PDBe:3d3z, PDBj:3d3z
• PDBsum: 3d3z
• UniProt: Q45U61