2VRF

CRYSTAL STRUCTURE OF THE HUMAN BETA-2-SYNTROPHIN PDZ DOMAIN

PDB DOI: https://doi.org/10.2210/pdb2VRF/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-03-31 Released: 2008-04-22
Deposition Author(s): Sun, Z., Roos, A.K., Pike, A.C.W., Pilka, E.S., Cooper, C., Elkins, J.M., Murray, J., Arrowsmith, C.H., Doyle, D., Edwards, A., von Delft, F., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.247 (Depositor), 0.250 (DCC)
R-Value Work:
0.184 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Human Beta-2-Syntrophin Pdz Domain

Sun, Z., Roos, A.K., Pike, A.C.W., Pilka, E.S., Cooper, C., Elkins, J.M., Murray, J., Arrowsmith, C.H., Doyle, D., Edwards, A., von Delft, F., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 41.57 kDa
Atom Count: 3,034
Modelled Residue Count: 380
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-SYNTROPHIN	A, B, C, D	95	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13425 (Homo sapiens) Explore Q13425 Go to UniProtKB: Q13425
PHAROS: Q13425 GTEx: ENSG00000168807
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13425
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth C]	E [auth A], F [auth A], G [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247 (Depositor), 0.250 (DCC)
R-Value Work: 0.184 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.687	α = 90
b = 29.503	β = 95.78
c = 128.382	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2012-12-05
Changes: Database references, Derived calculations, Other, Structure summary
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description