Research workbench
Crystal structure of UBA4-URM1 from chaetomium thermophilum
Analyse Crystal structure of UBA4-URM1 from chaetomium thermophilum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YUC
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylyltransferase and sulfurtransferase UBA4; Ubiquitin-related modifier 1
- EC
- 2.7.7.80, 2.8.1.11
- UniProt
- G0SC54, G0SE11
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Adenylyltransferase and sulfurtransferase UBA4 (EC 2.7.7.80, 2.8.1.11) | protein | 285 | 33% helix, 17% strand | G0SC54 |
| G | Ubiquitin-related modifier 1 | protein | 100 | 16% helix, 29% strand | G0SE11 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.57 | 0.83 | 27 | empty |
| 2 | 125 | 0.57 | 0.83 | 23 | empty |
| 3 | 62 | 0.48 | 0.85 | 21 | empty |
| 4 | 71 | 0.36 | 0.77 | 19 | empty |
| 5 | 59 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- D–G · 1159 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6YUC · Crystal structure of Uba4-Urm1 from Chaetomium thermophilum · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt G0SC54
- Every structure of UniProt G0SE11
- Elsewhere: RCSB PDB 6YUC · PDBe 6YUC · UniProt G0SC54 · UniProt G0SE11
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