2F16

Crystal structure of the yeast 20S proteasome in complex with bortezomib

Structural Biology Knowledgebase: 2F16 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.231

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F16

Classification: hydrolase

Total Structure Weight: 706516.88

Macromolecule Entities
Molecule Chains Length Organism Details
Proteasome component Y7 A, O 250 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE8 PRS4 YML092C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component Y13 B, P 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE9 PRS5 YGR135W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE6 C, Q 241 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE6 YOL038W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP2 D, R 242 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP2 DOA5 YGR253C G9155
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE5 E, S 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE5 YMR314W YM9924.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C1 F, T 244 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE10 PRC1 Gene View PRS1 YOR362C O6650
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C7-alpha G, U 243 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): SCL1 PRC2 PRS2 YGL011C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP1 H, V 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP1 YOR157C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PUP3 I, W 204 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PUP3 YER094C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C11 J, X 198 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE1 YER012W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE2 K, Y 212 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE2 DOA3 PRG1 YPR103W P8283.10
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component C5 L, Z 222 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE7 PRS3 PTS1 YBL041W YBL0407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE4 1, M 233 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE4 YFR050C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Proteasome component PRE3 2, N 196 Saccharomyces cerevisiae EC#: 3.4.25.1 IUBMB
Gene Name(s): PRE3 YJL001W J1407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BO2
Query on BO2

2, H, K, N, V, Y N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]- N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
BORTEZOMIB (Synonym)
C19 H25 B N4 O4
GXJABQQUPOEUTA-RDJZCZTQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.231
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 136.18 α = 90.00
b = 300.72 β = 113.28
c = 144.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-14
  • Released Date: 2006-03-21
  • Deposition author(s): Groll, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values