1YF9 | pdb_00001yf9

Structural analysis of Leishmania major ubiquitin conjugating enzyme E2

PDB DOI: https://doi.org/10.2210/pdb1YF9/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-12-31 Released: 2005-02-22
Deposition Author(s): Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.210 (Depositor), 0.219 (DCC)
R-Value Work:
0.185 (Depositor), 0.191 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural Analysis of Leishmania major ubiquitin conjugating enzyme E2

Bosch, J., Hol, W.G.J.

To be published.

Macromolecule Content

Total Structure Weight: 58.69 kDa
Atom Count: 4,338
Modeled Residue Count: 477
Deposited Residue Count: 513
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carrier protein 4	A, B, C	171	Leishmania major	Mutation(s): 0
UniProt
Find proteins for Q4Q5L3 (Leishmania major) Explore Q4Q5L3 Go to UniProtKB: Q4Q5L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4Q5L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth C] D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.210 (Depositor), 0.219 (DCC)
R-Value Work: 0.185 (Depositor), 0.191 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.448	α = 90
b = 114.448	β = 90
c = 139.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXS	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-02-22

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2005-02-22
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description

1YF9 | pdb_00001yf9

Structural analysis of Leishmania major ubiquitin conjugating enzyme E2

Literature

Structural Analysis of Leishmania major ubiquitin conjugating enzyme E2

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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