6NEW | pdb_00006new

Apo structure of the activated truncation of Vav1

PDB DOI: https://doi.org/10.2210/pdb6NEW/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-18 Released: 2019-12-25
Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.256 (DCC)
R-Value Work:
0.199 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Allosteric Inhibitors of VAV1 Block Guanine Nucleotide Exchange Activity

Gerspacher, M., Skaanderup, P.R.

To be published.

Macromolecule Content

Total Structure Weight: 49.81 kDa
Atom Count: 3,313
Modeled Residue Count: 389
Deposited Residue Count: 421
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene vav	A	421	Homo sapiens	Mutation(s): 0 Gene Names: VAV1, VAV
UniProt & NIH Common Fund Data Resources
Find proteins for P15498 (Homo sapiens) Explore P15498 Go to UniProtKB: P15498
PHAROS: P15498 GTEx: ENSG00000141968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15498
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.257 (Depositor), 0.256 (DCC)
R-Value Work: 0.199 (Depositor), 0.204 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.925	α = 90
b = 67.693	β = 90
c = 178.56	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.