MolNFT v1 · #181181 · protein
Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated ub-eos (chapso, class 2, open state)
7LN6 · Transitional endoplasmic reticulum ATPase: “Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated ub-eos (chapso, class 2, open…”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability…
- PDB
- 7LN6
- Type
- protein
- Length
- 4,456 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 0.84
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 | 731 | 45% helix, 17% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 741 | 42% helix, 17% strand | P55072 |
| C, D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 752 | 41% helix, 17% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 743 | 44% helix, 16% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 714 | 45% helix, 16% strand | P55072 |
| G | Polyubiquitinated ub-eos | protein | 23 | 0% helix, 22% 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 | 1137 | 0.84 | 0.85 | 94 | empty |
| 2 | 972 | 0.82 | 0.84 | 80 | ATP, MG |
| 3 | 932 | 0.82 | 0.84 | 77 | ATP, MG |
| 4 | 569 | 0.82 | 0.88 | 70 | ATP, MG |
| 5 | 626 | 0.81 | 0.86 | 70 | ATP, MG |
Interfaces
19 interfaces between chains.
- D–E · 5781 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 5555 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 5171 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 4052 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 3483 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7LN6 · 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 7LN6 · PDBe 7LN6 · UniProt P55072
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