2NSQ | pdb_00002nsq

Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein

PDB DOI: https://doi.org/10.2210/pdb2NSQ/pdb

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

Deposited: 2006-11-06 Released: 2006-12-19
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.218 (Depositor), 0.226 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein

Walker, J.R., Avvakumov, G.V., Xue, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.09 kDa
Atom Count: 1,275
Modeled Residue Count: 140
Deposited Residue Count: 155
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase NEDD4-like protein	A	155	Homo sapiens	Mutation(s): 0 Gene Names: NEDD4L, KIAA0439, NEDL3 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU5 (Homo sapiens) Explore Q96PU5 Go to UniProtKB: Q96PU5
PHAROS: Q96PU5 GTEx: ENSG00000049759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96PU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.218 (Depositor), 0.226 (DCC)
R-Value Work: 0.171 (Depositor), 0.177 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.93	α = 90
b = 60.036	β = 90
c = 74.51	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2013-08-28
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description