3W04

Crystal structure of Oryza sativa DWARF14 (D14)

Structural Biology Knowledgebase: 3W04 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.160

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3W04

Classification: HYDROLASE

Total Structure Weight: 59292.62

Macromolecule Entities
Molecule Chains Length Organism Details
Dwarf 88 esterase A, B 266 Oryza sativa EC#: 3.1 IUBMB
Fragment: UNP residues 55-318
Gene Name(s): D14 D88 HTD2 Os03g0203200 LOC_Os03g10620

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

B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A, B (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.160
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.99 α = 90.00
b = 88.19 β = 90.00
c = 121.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-19
  • Released Date: 2013-01-23
  • Deposition author(s): Kagiyama, M., Hirano, Y., Mori, T., Kim, S.Y., Kyozuka, J., Seto, Y., Yamaguchi, S., Hakoshima, T.

Revision History

  • 2013-02-06
    Type: Citation | Details: Citation update