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Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated ub-eos (chapso, class 1, close state)
Analyse Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LN5
- Type
- protein
- Length
- 4,447 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase; Polyubiquitinated ub-eos
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 6 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 | 43% helix, 16% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 743 | 43% helix, 16% strand | P55072 |
| C, D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 752 | 43% helix, 17% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 743 | 44% helix, 17% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 703 | 44% helix, 17% strand | P55072 |
| G | Polyubiquitinated ub-eos | protein | 22 | 0% helix, 36% 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 | 854 | 0.82 | 0.85 | 80 | ATP, MG |
| 2 | 1157 | 0.82 | 0.83 | 97 | ATP |
| 3 | 516 | 0.82 | 0.89 | 57 | ATP, MG |
| 4 | 912 | 0.81 | 0.84 | 81 | ATP, MG |
| 5 | 769 | 0.81 | 0.84 | 69 | empty |
Interfaces
16 interfaces between chains.
- D–E · 5737 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 5541 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 5116 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3918 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 3020 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7LN5 · Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos… · the same entry in another collection · chain A against A, 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 P55072
- Elsewhere: RCSB PDB 7LN5 · PDBe 7LN5 · UniProt P55072
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