1Z2B

Tubulin-colchicine-vinblastine: stathmin-like domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.209

Literature

Macromolecules
Sequence Display for 1Z2B

Classification: CELL CYCLE

Total Structure Weight: 220138.09

Macromolecule Entities
Molecule Chains Length Organism Details
Tubulin alpha chain A, C 448 Bos taurus Mutation: V7I, M16I, T50N, C54S, I78V, N80T, P82T, P117L, S126A, S232G, A334T
Gene Name(s): TUBA1D
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Tubulin beta chain B, D 445 Bos taurus Mutation: M172V, I318V
Gene Name(s): TUBB2B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RB3 STATHMIN-LIKE DOMAIN 4 E 142 Rattus norvegicus Gene Name(s): Stmn4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VLB
Query on VLB

C (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE
VINBLASTINE (Synonym)
C46 H58 N4 O9
JXLYSJRDGCGARV-CFWMRBGOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GTP
Query on GTP

A, C GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GDP
Query on GDP

B, D GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CN2
Query on CN2

B, D 2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO- 5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE
C22 H25 N O6 S
TYDIWMTWTXFWSY-HNNXBMFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VLB IC50: 1.1 nM (98) BindingDB
Ki: >100000 nM (99) BindingDB

N/A in BindingMoad
Kd: 400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.209
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 324.85 α = 90.00
b = 324.85 β = 90.00
c = 54.21 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-03-08
  • Released Date: 2005-05-31
  • Deposition author(s): Gigant, B., Wang, C., Ravelli, R.B.G., Roussi, F., Steinmetz, M.O., Curmi, P.A., Sobel, A., Knossow, M.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Advisory, Version format compliance