MolNFT v1 · #181177 · protein
Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated ub-eos (fom, class 1)
7LN2 · Transitional endoplasmic reticulum ATPase: “Cryo-EM structure of human P97 in complex with NPL4/UFD1 and polyubiquitinated ub-eos (fom, class 1)”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.84).…
- PDB
- 7LN2
- Type
- protein
- Length
- 4,433 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 · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 732 | 43% helix, 17% strand | P55072 |
| B | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 743 | 45% helix, 16% strand | P55072 |
| C, D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 752 | 43% helix, 16% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 732 | 45% helix, 16% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 700 | 45% helix, 16% strand | P55072 |
| G | Polyubiquitinated ub-eos | protein | 22 | 0% helix, 27% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 7 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, F, B, E
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E
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 | 1125 | 0.84 | 0.85 | 106 | ATP, MG |
| 2 | 983 | 0.84 | 0.85 | 106 | ATP, MG |
| 3 | 634 | 0.83 | 0.88 | 75 | ATP, MG |
| 4 | 577 | 0.83 | 0.89 | 69 | ATP, MG |
| 5 | 1117 | 0.82 | 0.83 | 93 | ATP, MG |
Interfaces
19 interfaces between chains.
- D–E · 5620 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 5533 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 5111 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3917 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 2389 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7LN2 · 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 7LN2 · PDBe 7LN2 · UniProt P55072
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