2C54

GDP-MANNOSE-3', 5' -EPIMERASE (ARABIDOPSIS THALIANA), K178R, WITH GDP-BETA-L-GULOSE AND GDP-4-KETO-BETA-L-GULOSE BOUND IN ACTIVE SITE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.167
  • R-Value Work: 0.118

Literature

Macromolecules
Sequence Display for 2C54

Classification: ISOMERASE

Total Structure Weight: 90754.93

Macromolecule Entities
Molecule Chains Length Organism Details
GDP-MANNOSE-3', 5'-EPIMERASE A, B 379 Arabidopsis thaliana EC#: 5.1.3.18 IUBMB
Mutation: K178R
Details: GDP-BETA-L-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND GULOSE-MONOPHOSPHATE (GUL), LINKING THE GDP O3A TO THE GUL PB. GDP-BETA-L-4-KETO-GULOSE WAS REFINED USING GMP (DEFINED AS GDP, MODIFIED IN THE CIF FILE TO REMOVE THE SECOND PHOSPHATE GROUP) AND 4-KETO-GULOSE- MONOPHOSPHATE (4KG), LINKING THE GDP O3A TO THE 4KG PB NAD WAS REFINED USING ADP AND A NICOTINAMIDE RING (NI3), LINKING THE ADP PB TO THE NI3 O5* NADH WAS REFINED USING ADP AND A SKEWED REDUCED NICOTINAMIDE RING (NDH), LINKING THE ADP PB TO THE NDH O5*
Gene Name(s): At5g28840 F7P1.20
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GKE
Query on GKE

A, B GUANOSINE 5'-DIPHOSPHATE-BETA-L-GULOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-HVMPVDAASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GKD
Query on GKD

A, B GUANOSINE 5'-DIPHOSPHATE-4-KETO-BETA-L-GULOSE
C16 H23 N5 O16 P2
QZZKIVADHWVJFF-UFFCYROPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

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

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.167
  • R-Value Work: 0.118
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 62.28 α = 90.00
b = 82.46 β = 98.77
c = 65.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-25
  • Released Date: 2005-11-14
  • Deposition author(s): Major, L.L., Wolucka, B.A., Naismith, J.H.

Revision History

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