2C7V

STRUCTURE OF TRYPANOSOMA BRUCEI PTERIDINE REDUCTASE (PTR1) IN TERNARY COMPLEX WITH COFACTOR AND THE ANTIFOLATE METHOTREXATE

Structural Biology Knowledgebase: 2C7V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2C7V

Classification: OXIDOREDUCTASE

Total Structure Weight: 119981.23

Macromolecule Entities
Molecule Chains Length Organism Details
PTERIDINE REDUCTASE A, B, C, D 268 Trypanosoma brucei EC#: 1.5.1.33 IUBMB
Gene Name(s): PTR1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A, B, C, D NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MTX
Query on MTX

A, B, C, D METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
MTX N/A in BindingDB
Ki: 152 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CAF
Query on CAF
A, B, C, D L-PEPTIDE LINKING C5 H12 As N O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.153
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.65 α = 90.00
b = 90.24 β = 115.76
c = 82.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-29
  • Released Date: 2006-09-19
  • Deposition author(s): Dawson, A., Gibellini, F., Sienkiewicz, N., Fyfe, P.K., Mcluskey, K., Fairlamb, A.H., Hunter, W.N.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4