4IMA

The structure of C436M-hLPYK in complex with Citrate/Mn/ATP/Fru-1,6-BP

Structural Biology Knowledgebase: 4IMA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IMA

Classification: TRANSFERASE

Total Structure Weight: 236933.14

Macromolecule Entities
Molecule Chains Length Organism Details
Pyruvate kinase A, B, C, D 543 Homo sapiens EC#: 2.7.1.40 IUBMB
Fragment: UNP residues 57-599
Mutation: C436M
Gene Name(s): PKLR Gene View PK1 PKL

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

A, B, C, D BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE (Synonym)
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADN
Query on ADN

D ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FLC
Query on FLC

A, B, C, D CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.75 α = 90.00
b = 204.73 β = 96.75
c = 86.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-02
  • Released Date: 2013-01-23
  • Deposition author(s): Zhang, B., Holyoak, T., Fenton, A.W., Tang, Q.L., Prasannan, C.B., Deng, J.P.

Revision History

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