4GI7

Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue

Structural Biology Knowledgebase: 4GI7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GI7

Classification: TRANSFERASE

Total Structure Weight: 312653.26

Macromolecule Entities
Molecule Chains Length Organism Details
Pantothenate kinase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 334 Klebsiella pneumoniae EC#: 1.2.1.8 IUBMB 2.7.1.33 IUBMB
Gene Name(s): coaA KPK_5321

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

A, B, C, D, E, F, G, H ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
0JR
Query on 0JR

A, B, C, D, F (2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo- 3-[(pyridin-3-ylmethyl)amino]propyl}butanamide
C15 H23 N3 O4
VXNNKPMWKMAMDX-ZDUSSCGKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A, B, C, D, E, F, G, H UNKNOWN ATOM OR ION
X
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000903 (BAL,PAF,0YC) A, B, C, D, F (2R)-2,4-DIHYDROXY-3,3-DIMETHYL-N-{3-OXO-3-[(PYRIDIN-3-YLMETHYL)AMINO]PROPYL}BUTANAMIDE Non-polymer /
Antibiotic, Antimicrobial
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.220
  • R-Value Work: 0.186
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 127.93 α = 90.00
b = 130.94 β = 90.00
c = 193.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-08
  • Released Date: 2013-04-10
  • Deposition author(s): Li, B., Tempel, W., Smil, D., Bolshan, Y., Hong, B.S., Park, H.W., Structural Genomics Consortium (SGC)

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update
  • 2013-04-17
    Type: Citation | Details: Citation update