Research workbench
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 3)
Analyse Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LN1
- Type
- protein
- Length
- 4,411 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- Transitional endoplasmic reticulum ATPase; Hexa-ubiquitin
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.4 · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 732 | 44% helix, 17% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 731 | 44% helix, 16% strand | P55072 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 741 | 43% helix, 17% strand | P55072 |
| D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 752 | 42% helix, 17% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 743 | 42% helix, 16% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 703 | 44% helix, 17% strand | P55072 |
| G | Hexa-ubiquitin | protein | 9 | 0% helix, 33% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, B, C
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F
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 | 973 | 0.83 | 0.84 | 95 | ATP |
| 2 | 507 | 0.83 | 0.89 | 69 | ATP, MG |
| 3 | 1126 | 0.82 | 0.84 | 115 | ATP, MG |
| 4 | 1009 | 0.82 | 0.83 | 89 | ATP, MG |
| 5 | 451 | 0.82 | 0.89 | 67 | ATP, MG |
Interfaces
16 interfaces between chains.
- D–E · 5708 Ų buried · 60 hydrogen bonds · protein-protein
- C–D · 5167 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 4371 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 3836 Ų buried · 37 hydrogen bonds · protein-protein
- A–F · 3153 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7LN1 · Cryo-EM structure of human P97 in complex with NPL4/UFD1 and UB6 (class 3) · the same entry in another collection · chain G against G, TM-score 1.00
- P55072 · AlphaFold monomer V2.0 prediction for transitional endoplasmic reticulum ATPase (P55072) · a predicted model of the same protein · chain B against A, TM-score 0.78
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
- Elsewhere: RCSB PDB 7LN1 · PDBe 7LN1 · UniProt P55072
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