1M5Q

Crystal structure of a novel Sm-like archaeal protein from Pyrobaculum aerophilum

Structural Biology Knowledgebase: 1M5Q SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1M5Q

Classification: TRANSLATION

Total Structure Weight: 425491.84

Macromolecule Entities
Molecule Chains Length Organism Details
small nuclear ribonucleoprotein homolog 1, 2, A..., B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z 130 Pyrobaculum aerophilum Gene Name(s): PAE2122
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

1, 2, A, B, D, E, F, H, I, J, K, L, M, O, P, Q, R, S, U, V, W, X, Y, Z CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

1, 2, A, G, H, J, M, R, V, W, X GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

1, 2, F, H, I, K, M, N, V, W, X, Y, Z ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, R, S, V SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.191
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.32 α = 90.00
b = 172.43 β = 90.00
c = 148.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-09
  • Released Date: 2003-03-18
  • Deposition author(s): Mura, C., Phillips, M., Kozhukhovsky, A., Eisenberg, D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update