1K1E

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Structural Biology Knowledgebase: 1K1E SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1K1E

Classification: HYDROLASE

Total Structure Weight: 239446.59

Macromolecule Entities
Molecule Chains Length Organism Details
deoxy-D-mannose-octulosonate 8-phosphate phosphatase A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 180 Haemophilus influenzae EC#: 3.1.3.45 IUBMB
Gene Name(s): HI_1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H, I, J, K, L MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

C, H, J 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F, G, H, I, J, K, L SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, C, G, I, K GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CO
Query on CO

A, B, C, D, E, F, G, H, I, J, K, L COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.178
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.30 α = 90.00
b = 109.10 β = 107.60
c = 179.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-25
  • Released Date: 2002-02-27
  • Deposition author(s): Lim, K., Herzberg, O., Structure 2 Function Project (S2F)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name