5YY4

Crystal structure of the scFv antibody 4B08 with sulfated epitope peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tyrosine Sulfation Restricts the Conformational Ensemble of a Flexible Peptide, Strengthening the Binding Affinity for an Antibody

Miyanabe, K.Yamashita, T.Abe, Y.Akiba, H.Takamatsu, Y.Nakakido, M.Hamakubo, T.Ueda, T.Caaveiro, J.M.M.Tsumoto, K.

(2018) Biochemistry 57: 4177-4185


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
scFv 4B08
A
252N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-C chemokine receptor type 5
B
9Homo sapiensMutation(s): 0 
Gene Names: CCR5 (CMKBR5)
Find proteins for P51681 (Homo sapiens)
Go to Gene View: CCR5
Go to UniProtKB:  P51681
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.250α = 90.00
b = 56.610β = 90.00
c = 97.920γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25249115
Japan Society for the Promotion of ScienceJapan15K06962

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references
  • Version 1.2: 2018-08-01
    Type: Data collection, Database references