MolNFT v1 · #114825 · protein
P97-DELTA709-728 in complex with a UFD1-shp peptide
5C1B · Transitional endoplasmic reticulum ATPase: “P97-DELTA709-728 in complex with a UFD1-shp peptide”. X-ray diffraction, 3 ligands (AGS, MG, CL), 20 pockets (best druggability 0.85). MolNFT v1 #114825 on GenesisL1: 3D structure, binding…
- PDB
- 5C1B
- Type
- protein
- Length
- 4,365 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase; Ubiquitin fusion degradation protein 1 homolog
- EC
- 3.6.4.6
- UniProt
- P55072, Q92890
- Ligands
- AGS, MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 724 | 45% helix, 18% strand | P55072 |
| V | Ubiquitin fusion degradation protein 1 homolog | protein | 11 | 0% helix, 0% strand | Q92890 |
| U | Ubiquitin fusion degradation protein 1 homolog | protein | 10 | 0% helix, 0% strand | Q92890 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 975 | 0.85 | 0.87 | 121 | AGS, MG |
| 2 | 666 | 0.83 | 0.87 | 75 | empty |
| 3 | 632 | 0.82 | 0.87 | 84 | AGS, MG |
| 4 | 552 | 0.81 | 0.87 | 78 | empty |
| 5 | 531 | 0.81 | 0.87 | 75 | AGS, MG |
Interfaces
8 interfaces between chains.
- D–E · 4040 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3969 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3838 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3809 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 3720 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5C1B · p97-delta709-728 in complex with a UFD1-SHP peptide · the same entry in another collection · chain U against U, TM-score 1.00
- Q92890 · AlphaFold monomer V2.0 prediction for ubiquitin recognition factor in er-associated… · a predicted model of the same protein · chain U against A, TM-score 0.33
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 Q92890
- Elsewhere: RCSB PDB 5C1B · PDBe 5C1B · UniProt P55072 · UniProt Q92890
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