MolNFT v1 · #186659 · protein
Cryo-EM structure of human P97-E470D mutant bound to ADP.
7RLD · Transitional endoplasmic reticulum ATPase: “Cryo-EM structure of human P97-E470D mutant bound to ADP.”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.84). MolNFT v1 #186659 on GenesisL1: 3D structure, binding…
- PDB
- 7RLD
- Type
- protein
- Length
- 4,410 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 37% helix, 14% 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 | 735 | 37% helix, 14% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, F, 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 | 770 | 0.84 | 0.88 | 116 | ADP |
| 2 | 917 | 0.83 | 0.85 | 109 | ADP |
| 3 | 1049 | 0.81 | 0.82 | 91 | ADP |
| 4 | 1021 | 0.81 | 0.82 | 97 | ADP |
| 5 | 993 | 0.81 | 0.82 | 92 | ADP |
Interfaces
6 interfaces between chains.
- E–F · 3619 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 3609 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 3596 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 3595 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3542 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7RLD · Cryo-EM structure of human p97-E470D mutant bound to ADP. · 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 7RLD · PDBe 7RLD · UniProt P55072
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