Download MendeleyCrystal structure of human SUMO complex
Reiter, K.H., Boucher, L.E., Bosch, J., Matunis, M.J.To be published.
4W5V
Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd)
- PDB DOI: 10.2210/pdb4W5V/pdb
- Classification: LIGASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-08-19 Released: 2015-09-09
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.283
- R-Value Work: 0.221
- R-Value Observed: 0.224
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| SUMO-conjugating enzyme UBC9 | A | 163 | Homo sapiens | Mutation(s): 0 Gene Names: UBE2I, UBC9, UBCE9 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P63279 (Homo sapiens) Explore P63279 Go to UniProtKB: P63279 | |||||
PHAROS: P63279 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P63279 | ||||
Protein Feature ViewExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SUMO-activating enzyme subunit 2 | B | 122 | Homo sapiens | Mutation(s): 0 Gene Names: UBA2, SAE2, UBLE1B, HRIHFB2115 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt) |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9UBT2 (Homo sapiens) Explore Q9UBT2 Go to UniProtKB: Q9UBT2 | |||||
PHAROS: Q9UBT2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9UBT2 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| FMT Query on FMT | C [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | Ligand Interaction | |
| K Query on K | E [auth B] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.283
- R-Value Work: 0.221
- R-Value Observed: 0.224
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 161.273 | α = 90 |
| b = 35.272 | β = 96.69 |
| c = 58.672 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| XDS | data reduction |
| XDS | data scaling |
| XSCALE | data scaling |
| Blu-Ice | data collection |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2014-08-19
- Released Date: 2015-09-09 Deposition Author(s): Boucher, L.E., Reiter, K.H., Matunis, M.J., Bosch, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM060980 |
Revision History (Full details and data files)
- Version 1.0: 2015-09-09
Type: Initial release - Version 1.1: 2017-09-06
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2019-12-25
Changes: Author supporting evidence
