4NKT

Structure of Cid1 in complex with the UTP analog UMPNPP

Structural Biology Knowledgebase: 4NKT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4NKT

Classification: TRANSFERASE

Total Structure Weight: 79273.38

Macromolecule Entities
Molecule Chains Length Organism Details
Poly(A) RNA polymerase protein cid1 A, B 341 Schizosaccharomyces pombe EC#: 2.7.7 IUBMB
Fragment: UNP residues 40-377
Mutation: D160A
Gene Name(s): cid1 SPAC19D5.03

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

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

A, B BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2KH N/A in BindingDB
N/A in BindingMoad
Kd: 1080 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.179
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 53.77 α = 90.00
b = 77.32 β = 90.86
c = 82.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-11-13
  • Released Date: 2013-12-18
  • Deposition author(s): Munoz-Tello, P., Gabus, C., Thore, S.

Revision History

  • 2014-03-26
    Type: Citation | Details: Citation update
  • 2014-01-15
    Type: Citation | Details: Citation update