3W3S

Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS

Structural Biology Knowledgebase: 3W3S SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.204

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3W3S

Classification: LIGASE / RNA

Total Structure Weight: 98247.82


Macromolecule Entities
Molecule Chains Length Organism Details
Type-2 serine--tRNA ligase A 527 Methanopyrus kandleri EC#: 6.1.1.11 IUBMB
Mutation: R55Y, E58Y, E62Y, R116Y, D118Y, E189R, D193R, E379Y, E383R, E497Y, E499Y
Gene Name(s): serS MK1460
Macromolecule Entities
Molecule Chains Length Organism Details
selenocysteine tRNA B 99 Aquifex aeolicus

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

A 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PT
Query on PT

A PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.204
  • Space Group: I 4 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 272.82 α = 90.00
b = 272.82 β = 90.00
c = 272.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-27
  • Released Date: 2013-02-13
  • Deposition author(s): Itoh, Y., Sekine, S., Yokoyama, S.

Revision History

  • 2013-08-07
    Type: Citation | Details: Citation update
  • 2013-05-22
    Type: Citation | Details: Citation update