1Z2U | pdb_00001z2u

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

PDB DOI: https://doi.org/10.2210/pdb1Z2U/pdb

Classification: LIGASE
Organism(s): Caenorhabditis elegans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-03-09 Released: 2005-03-22
Deposition Author(s): Gavira, J.A., DiGiamamarino, E., Tempel, W., Liu, Z.J., Wang, B.C., Meehan, E., Ng, J.D., Southeast Collaboratory for Structural Genomics (SECSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.149 (Depositor), 0.158 (DCC)
R-Value Work:
0.131 (Depositor), 0.140 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The 1.1A crystallographic structure of ubiquitin-conjugating enzyme (ubc-2) from Caenorhabditis elegans: functional and evolutionary significance

Gavira, J.A., DiGiamamarino, E., Tempel, W., Liu, Z.J., Wang, B.C., Meehan, E., Ng, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 17.42 kDa
Atom Count: 1,409
Modeled Residue Count: 150
Deposited Residue Count: 150
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 2	A	150	Caenorhabditis elegans	Mutation(s): 0 Gene Names: ubc-2, let-70 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P35129 (Caenorhabditis elegans) Explore P35129 Go to UniProtKB: P35129
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35129
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BU3 Query on BU3 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.149 (Depositor), 0.158 (DCC)
R-Value Work: 0.131 (Depositor), 0.140 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.604	α = 90
b = 60.457	β = 106.45
c = 43.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
MAR345	data collection
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-22

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

Revision History (Full details and data files)

Version 1.0: 2005-03-22
Type: Initial release
Version 1.1: 2008-04-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description