4PR9 | pdb_00004pr9

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 (Depositor), 0.271 (DCC)
R-Value Work:
0.204 (Depositor), 0.236 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

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
Modeled Residue Count: 1,033
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 H [auth B] SDF format, chain K [auth E] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth E] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth E] mmCIF format, chain G [auth A]	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] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF 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 (Depositor), 0.271 (DCC)
R-Value Work: 0.204 (Depositor), 0.236 (DCC)
R-Value Observed: 0.206 (Depositor)

Diffraction Data:

Space Group: P 3₂ 1 2

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

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

4PR9 | pdb_00004pr9

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

Literature

Mechanism and function of lipid-directed oligomerization of vinculin

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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