4QAF

Crystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of an Anticalin with specific blocking activity towards human vascular endothelial growth factor (VEGF) reveals plasticity of the lipocalin fold

Giese, T.Skerra, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipocalin-1
A, B
152Homo sapiensMutation(s): 27 
Gene Names: LCN1 (VEGP)
Find proteins for P31025 (Homo sapiens)
Go to Gene View: LCN1
Go to UniProtKB:  P31025
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
C, D
112Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
OMA
Query on OMA

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Download CCD File 
A, B
10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid
C19 H34 O2
MGOIQHKBDDJUJK-XVSUHRFUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.210α = 90.00
b = 88.210β = 90.00
c = 103.421γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
MAR345dtbdata collection
XSCALEdata scaling
Auto-Rickshawphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-05-04 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Giese, T., Skerra, A.

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release