Research workbench
Structural insights into the interaction of P97 N-terminal domain and shp motif in derlin-1 rhomboid pseudoprotease
Analyse Structural insights into the interaction of P97 N-terminal domain and shp motif… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GLF
- Type
- protein
- Length
- 721 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase; Derlin-1
- EC
- 3.6.4.6
- UniProt
- P55072, Q9BUN8
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 170 | 16% helix, 41% strand | P55072 |
| B | Derlin-1 | protein | 12 | 0% helix, 25% strand | Q9BUN8 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 171 | 15% helix, 37% strand | P55072 |
| D | Derlin-1 | protein | 11 | 0% helix, 27% strand | Q9BUN8 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 169 | 16% helix, 40% strand | P55072 |
| F, H | Derlin-1 | protein | 10 | 0% helix, 30% strand | Q9BUN8 |
| G | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 168 | 15% helix, 41% strand | P55072 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.72 | 0.99 | 17 | empty |
| 2 | 547 | 0.68 | 0.78 | 51 | empty |
| 3 | 491 | 0.68 | 0.79 | 51 | empty |
| 4 | 336 | 0.58 | 0.76 | 35 | empty |
| 5 | 98 | 0.34 | 0.73 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–B · 759 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 757 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 718 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 714 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 647 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5GLF · Structural insights into the interaction of p97 N-terminal domain and SHP motif in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BUN8 · AlphaFold monomer V2.0 prediction for derlin-1 (Q9BUN8) · a predicted model of the same protein · chain H against A, TM-score 0.39
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 P55072
- Every structure of UniProt Q9BUN8
- Elsewhere: RCSB PDB 5GLF · PDBe 5GLF · UniProt P55072 · UniProt Q9BUN8
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