3QTK

The crystal structure of chemically synthesized VEGF-A

PDB DOI: https://doi.org/10.2210/pdb3QTK/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2011-02-22 Released: 2011-07-27
Deposition Author(s): Mandal, K., Kent, S.B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.182

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Total chemical synthesis of biologically active vascular endothelial growth factor.

Mandal, K., Kent, S.B.

(2011) Angew Chem Int Ed Engl 50: 8029-8033

PubMed: 21744452 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.201103237
Primary Citation of Related Structures:
3QTK

PubMed Abstract:
Efficient access: the 204-residue covalent-dimer vascular endothelial growth factor with full mitogenic activity was prepared from three unprotected peptide segments by one-pot native chemical ligations. The covalent structure of the synthetic VEGF was confirmed by precise mass measurement, and the three-dimensional structure of the synthetic protein was determined by high-resolution X-ray crystallography.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, IL 60637, USA.

Macromolecule Content

Total Structure Weight: 73.22 kDa
Atom Count: 5,274
Modelled Residue Count: 576
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A B [auth D] C [auth B] D [auth C] E A, B [auth D], C [auth B], D [auth C], E, F	102	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692 Go to UniProtKB: P15692
PHAROS: P15692 GTEx: ENSG00000112715
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15692
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TFA Query on TFA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth D] SDF format, chain O [auth B] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth D] MOL2 format, chain O [auth B] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth D] mmCIF format, chain O [auth B] mmCIF format, chain X [auth F]	H [auth A] J [auth A] K [auth A] M [auth D] O [auth B] H [auth A], J [auth A], K [auth A], M [auth D], O [auth B], X [auth F]	trifluoroacetic acid C₂ H F₃ O₂ DTQVDTLACAAQTR-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D] Focus chain O [auth B] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth D] Focus chain O [auth B] Focus chain X [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth D] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	I [auth A], N [auth D], R [auth C], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth D] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth D] Focus chain R [auth C] Focus chain S [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth C] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth F]	G [auth A] L [auth D] P [auth B] Q [auth C] T [auth C] G [auth A], L [auth D], P [auth B], Q [auth C], T [auth C], U [auth E], V [auth E], W [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth D] Focus chain P [auth B] Focus chain Q [auth C] Focus chain T [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain L [auth D] Focus chain P [auth B] Focus chain Q [auth C] Focus chain T [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.223
R-Value Work: 0.180
R-Value Observed: 0.182
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 230.922	α = 90
b = 44.008	β = 99.93
c = 73.111	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Mandal, K.

Kent, S.B.H.

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2012-10-17
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary