3BPU

Crystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant

PDB DOI: https://doi.org/10.2210/pdb3BPU/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-12-19 Released: 2008-01-08
Deposition Author(s): Pilka, E.S., Hozjan, V., Cooper, C., Pike, A.C.W., Elkins, J., Doyle, D.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.202 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (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 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant.

Pilka, E.S., Hozjan, V., Cooper, C., Pike, A.C.W., Elkins, J., Doyle, D.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 9.68 kDa
Atom Count: 712
Modelled Residue Count: 86
Deposited Residue Count: 88
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1	A	88	Homo sapiens	Mutation(s): 2 Gene Names: MAGI1, BAIAP1, BAP1, TNRC19
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QZ7 (Homo sapiens) Explore Q96QZ7 Go to UniProtKB: Q96QZ7
PHAROS: Q96QZ7 GTEx: ENSG00000151276
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96QZ7
Sequence Annotations Expand
Reference Sequence LOADING

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: 1.60 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.202 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.472	α = 90
b = 61.578	β = 90
c = 80.113	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: 2008-01-08

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-01-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description

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.