2PNK

CRYSTAL STRUCTURE OF AN URONATE ISOMERASE (BH0493) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.178
  • R-Value Work: 0.148

Literature

Macromolecules
Sequence Display for 2PNK

Classification: ISOMERASE

Total Structure Weight: 614806.56

Macromolecule Entities
Molecule Chains Length Organism Details
BH0493 protein A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 428 Bacillus halodurans Mutation: M1M, M25M, M56M, M69M, M142M, M215M, M220M, M257M, M258M, M281M, M300M, M320M, M328M, M337M, M340M, M342M, M344M
Gene Name(s): BH0493
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MPD
Query on MPD

C, G, K, L (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

C, D, F, K PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, D, E, G, H, I, J, K, L GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

F, I, L ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B, C, D, E, F, G, H, I, J, K, L FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, D, G, H, J, L CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, H, J SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNL
Query on UNL

Unknown ligand
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 273.72 α = 90.00
b = 158.56 β = 116.03
c = 181.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-04-24
  • Released Date: 2007-05-08
  • Deposition author(s): Joint Center for Structural Genomics (JCSG)

Revision History

  • Version 1_0: 2007-05-08

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Version format compliance

  • Version 1_3: 2017-10-18

    Type: Advisory, Refinement description

  • Version 1_4: 2017-10-25

    Type: Author supporting evidence