4DPG

Crystal Structure of Human LysRS: P38/AIMP2 Complex I

Structural Biology Knowledgebase: 4DPG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DPG

Classification: Ligase / APOPTOSIS

Total Structure Weight: 503817.33

Macromolecule Entities
Molecule Chains Length Organism Details
Lysine--tRNA ligase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 513 Homo sapiens EC#: 6.1.1.6 IUBMB
Fragment: UNP residues 70-581
Gene Name(s): KARS Gene View KIAA0070
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 I, J, K, L 54 Homo sapiens Fragment: UNP residues 1-48
Gene Name(s): AIMP2 Gene View JTV1 PRO0992

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ALA
Query on ALA

H ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Ligand Explorer
 
JSmol
APC
Query on APC

A, B, C, D, E, F, G, H DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE (Synonym)
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
Ligand Explorer
 
JSmol
LYS
Query on LYS

A, B, C, D, E, F, G, H LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
Ligand Explorer
 
JSmol
MG
Query on MG

A, B, C, D, E, F, G, H, J, L MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.185
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 79.20 α = 89.16
b = 122.01 β = 85.58
c = 149.20 γ = 89.71

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-13
  • Released Date: 2013-02-13
  • Deposition author(s): Fang, P., Wang, J., Bennett, S.P., Guo, M.

Revision History

No revisions since initial release