5A2K

Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 5A2K

Classification: IMMUNE SYSTEM

Total Structure Weight: 26992.66

Macromolecule Entities
Molecule Chains Length Organism Details
IG LAMBDA-1 CHAIN V REGION S43 H 244 Mus musculus Fragment: RESIDUES 6-115,20-129
Mutation: ΔT100, ΔG101, L108T, Q1002D, A1003I, T1078A, M1085I
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC P 6 Homo sapiens

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A2G
Query on A2G

P N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

H 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.176
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 35.42 α = 90.00
b = 68.80 β = 90.00
c = 90.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-05-20
  • Released Date: 2015-06-03
  • Deposition author(s): Martinez-Saez, N., Castro-Lopez, J., Valero-Gonzalez, J., Madariaga, D., Companon, I., Somovilla, V.J., Salvado, M., Asensio, J.L., Jimenez-Barbero, J., Avenoza, A., Busto, J.H., Bernardes, G.J.L., Peregrina, J.M., Hurtado-Guerrero, R., Corzana, F.

Revision History

  • Version 1_0: 2015-06-03

    Type: Initial release

  • Version 1_1: 2015-07-08

    Type: Database references

  • Version 1_2: 2015-08-26

    Type: Database references