4QAF | pdb_00004qaf

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

• PDB DOI: https://doi.org/10.2210/pdb4QAF/pdb

• Classification: TRANSPORT PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.6 kDa 
• Atom Count: 3,326 
• Modeled Residue Count: 389 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipocalin-1	A, D [auth B]	152	Homo sapiens	Mutation(s): 27  Gene Names: engineered variant, LCN1
UniProt & NIH Common Fund Data Resources
Find proteins for P31025 (Homo sapiens) Explore P31025  Go to UniProtKB:  P31025
PHAROS:  P31025 GTEx:  ENSG00000160349

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	B [auth C], C [auth D]	112	Homo sapiens	Mutation(s): 0  Gene Names: VEGFA, VEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
PHAROS:  P15692 GTEx:  ENSG00000112715

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OMA	E [auth A], J [auth B]	10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid C19 H34 O2 MGOIQHKBDDJUJK-XVSUHRFUSA-N
SO4	F [auth C], G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	I [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.21	α = 90
b = 88.21	β = 90
c = 103.421	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary