Download MendeleyCovalent Ubiquitin-USP2 Complex
Avvakumov, G.V., Walker, J.R., Bernstein, G., Xue, S., Finerty Jr., P.J., MacKenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.To be published.
2IBI | pdb_00002ibi
Covalent Ubiquitin-USP2 Complex
- PDB DOI: https://doi.org/10.2210/pdb2IBI/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2006-09-11 Released: 2006-10-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.259 (Depositor), 0.260 (DCC)
- R-Value Work: 0.190 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.194 (Depositor)
Starting Models: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 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 |
| Ubiquitin carboxyl-terminal hydrolase 2 | 374 | Homo sapiens | Mutation(s): 2 Gene Names: USP2, UBP41 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75604 (Homo sapiens) Explore O75604 Go to UniProtKB: O75604 | |||||
PHAROS: O75604 GTEx: ENSG00000036672 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O75604 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ubiquitin | 75 | Homo sapiens | Mutation(s): 0 Gene Names: Rps27a, UBA52, UBB, UBC |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48 | |||||
PHAROS: P0CG48 GTEx: ENSG00000150991 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0CG48 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| NEH Query on NEH | D [auth B] | ETHANAMINE C2 H7 N QUSNBJAOOMFDIB-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.259 (Depositor), 0.260 (DCC)
- R-Value Work: 0.190 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.194 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.839 | α = 90 |
| b = 54.4 | β = 107.66 |
| c = 75.021 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2006-10-24 Deposition Author(s): Walker, J.R., Avvakumov, G.V., Bernstein, G., Xue, S., Finerty Jr., P.J., MacKenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)
Revision History (Full details and data files)
- Version 1.0: 2006-10-24
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2021-10-20
Changes: Database references, Derived calculations - Version 1.4: 2023-08-30
Changes: Data collection, Refinement description
