Download MendeleyStructures of Leishmania naiffi uracil-DNA glycosylase in complex with several ligands identified with fragment cocktail crystallography.
Larson, E.T., Merritt, E.A.To be published.
3CXM
Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil
- PDB DOI: https://doi.org/10.2210/pdb3CXM/pdb
- Classification: HYDROLASE
- Organism(s): Leishmania naiffi
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2008-04-24 Released: 2008-05-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.160
- R-Value Work: 0.138
- R-Value Observed: 0.139
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Uracil-DNA glycosylase | 268 | Leishmania naiffi | Mutation(s): 0 Gene Names: similar to LbrM18_V2.0540 EC: 3.2.2 |  | |
UniProt | |||||
Find proteins for D0VWU0 (Leishmania naiffi) Explore D0VWU0 Go to UniProtKB: D0VWU0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VWU0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| URB Query on URB | C [auth A] | 5-bromopyrimidine-2,4(1H,3H)-dione C4 H3 Br N2 O2 LQLQRFGHAALLLE-UHFFFAOYSA-N |  | ||
| URA Query on URA | D [auth A] | URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| BR Query on BR | B [auth A] | BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.160
- R-Value Work: 0.138
- R-Value Observed: 0.139
- Space Group: P 61
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 75.32 | α = 90 |
| b = 75.32 | β = 90 |
| c = 105.703 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2008-05-06 Deposition Author(s): Larson, E.T., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
Revision History (Full details and data files)
- Version 1.0: 2008-05-06
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: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
