MolNFT v1 · #181999 · protein
Structure of human P97 ATPase L464P mutant
7MDM · Transitional endoplasmic reticulum ATPase: “Structure of human P97 ATPase L464P mutant”. Electron microscopy, 1 ligand (ADP), 20 pockets (best druggability 0.86). MolNFT v1 #181999 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7MDM
- Type
- protein
- Length
- 4,051 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 0.86
Structure
electron microscopy · 4 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 701 | 35% helix, 13% strand | P55072 |
| C, D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 703 | 36% helix, 15% strand | P55072 |
| E | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 704 | 33% helix, 13% strand | P55072 |
| F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 539 | 44% helix, 9% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains B, A, 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 | 1004 | 0.86 | 0.87 | 134 | ADP |
| 2 | 1196 | 0.86 | 0.87 | 164 | empty |
| 3 | 1190 | 0.85 | 0.87 | 142 | ADP |
| 4 | 569 | 0.83 | 0.89 | 84 | empty |
| 5 | 826 | 0.83 | 0.86 | 113 | ADP |
Interfaces
11 interfaces between chains.
- B–A · 3507 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 3373 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 3267 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 3192 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 3151 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7MDM · Structure of human p97 ATPase L464P mutant · 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 7MDM · PDBe 7MDM · UniProt P55072
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