5W0N

Structure of human TUT7 catalytic module (CM) in complex with UMPNPP and U2 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 5W0N

Classification: TRANSFERASE

Total Structure Weight: 143758.47

Macromolecule Entities
Molecule Chains Length Organism Details
Terminal uridylyltransferase 7 A, B, C 403 Homo sapiens EC#: 2.7.7.52 IUBMB
Fragment: nucleotidyltransferase domain (UNP residues 963-1365)
Gene Name(s): ZCCHC6 Gene View HS2 KIAA1711 TUT7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UPU
Query on UPU

A, B, C [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN- 1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]METHYL (2R,3S,4R,5R)-5-(2,4-DIOXO-3,4- DIHYDROPYRIMIDIN-1(2H)-YL)-4-HYDROXY-2-(HYDROXYMETHYL)TETRAHYDROFURAN- 3-YL HYDROGEN (S)-PHOSPHATE
C18 H23 N4 O14 P
KXSPLNAXPMVUEC-NCOIDOBVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
2KH
Query on 2KH

A, B, C 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
C9 H16 N3 O14 P3
OZIBFYOFLVBDIY-XVFCMESISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A, B, C IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.187
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 135.97 α = 90.00
b = 135.97 β = 90.00
c = 181.57 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-05-31
  • Released Date: 2017-06-28
  • Deposition author(s): Faehnle, C.R., Walleshauser, J., Joshua-Tor, L.

Revision History

  • 2017-07-19
    Type: Database references
  • 2017-08-16
    Type: Database references