Research workbench
Structural basis for UFM1 recognition by ufsp
Analyse Structural basis for UFM1 recognition by ufsp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XDA
- Type
- protein
- Length
- 3,732 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UFM1-specific protease; Ubiquitin-fold modifier 1
- EC
- 3.4.22.-
- UniProt
- Q94218, P34661
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UFM1-specific protease (EC 3.4.22.-) | protein | 537 | 31% helix, 25% strand | Q94218 |
| B | UFM1-specific protease (EC 3.4.22.-) | protein | 542 | 30% helix, 26% strand | Q94218 |
| C | UFM1-specific protease (EC 3.4.22.-) | protein | 541 | 31% helix, 25% strand | Q94218 |
| D | UFM1-specific protease (EC 3.4.22.-) | protein | 538 | 28% helix, 24% strand | Q94218 |
| E | UFM1-specific protease (EC 3.4.22.-) | protein | 535 | 31% helix, 24% strand | Q94218 |
| F | UFM1-specific protease (EC 3.4.22.-) | protein | 535 | 29% helix, 23% strand | Q94218 |
| G, H, I, J, K, L | Ubiquitin-fold modifier 1 | protein | 84 | 25% helix, 36% strand | P34661 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.85 | 0.86 | 78 | empty |
| 2 | 658 | 0.70 | 0.78 | 66 | empty |
| 3 | 591 | 0.70 | 0.78 | 61 | empty |
| 4 | 651 | 0.69 | 0.77 | 62 | empty |
| 5 | 573 | 0.68 | 0.77 | 50 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1416 Ų buried · 18 hydrogen bonds · protein-protein
- F–L · 1068 Ų buried · 23 hydrogen bonds · protein-protein
- B–H · 1063 Ų buried · 20 hydrogen bonds · protein-protein
- C–I · 1045 Ų buried · 22 hydrogen bonds · protein-protein
- E–K · 1037 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5XDA · Structural basis for Ufm1 recognition by UfSP · the same entry in another collection · chain L against L, 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 Q94218
- Every structure of UniProt P34661
- Elsewhere: RCSB PDB 5XDA · PDBe 5XDA · UniProt Q94218 · UniProt P34661
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