4PR9

Human Vinculin (residues 891-1066) in complex with PIP

PDB DOI: https://doi.org/10.2210/pdb4PR9/pdb

Classification: CELL ADHESION, STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-03-05 Released: 2014-12-10
Deposition Author(s): Chinthalapudi, K., Rangarajan, E.S., Patil, D., Izard, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.250
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Mechanism and function of lipid-directed oligomerization of vinculin

Chinthalapudi, K., Rangarajan, E.S., Patil, D., Izard, T.

To be published.

Macromolecule Content

Total Structure Weight: 120.56 kDa
Atom Count: 8,174
Modelled Residue Count: 1,033
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vinculin	A, B, C, D, E A, B, C, D, E, F	176	Homo sapiens	Mutation(s): 1 Gene Names: VCL
UniProt & NIH Common Fund Data Resources
Find proteins for P18206 (Homo sapiens) Explore P18206 Go to UniProtKB: P18206
PHAROS: P18206 GTEx: ENSG00000035403
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18206
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth E]	G [auth A], H [auth B], K [auth E]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain L [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth F]	I [auth B], J [auth C], L [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.250
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: P 3₂ 1 2
Diffraction Data: https://doi.org/10.15785/SBGRID/560

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.579	α = 90
b = 102.579	β = 90
c = 190.772	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-10
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

4PR9

Human Vinculin (residues 891-1066) in complex with PIP

Mechanism and function of lipid-directed oligomerization of vinculin

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)