Research workbench
Structure of human P97 in complex with atpgammas and NPL4/UFD1 (masked around P97)
Analyse Structure of human P97 in complex with atpgammas and NPL4/UFD1 (masked around… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JY5
- Type
- protein
- Length
- 4,386 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
- AGS, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 43% helix, 17% 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 | 731 | 43% helix, 17% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, F, B, C, D, E
- MG · Magnesium ion · metal · 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 | 791 | 0.84 | 0.87 | 115 | MG, AGS |
| 2 | 961 | 0.82 | 0.84 | 100 | empty |
| 3 | 893 | 0.82 | 0.84 | 123 | MG, AGS |
| 4 | 589 | 0.81 | 0.87 | 92 | MG, AGS |
| 5 | 514 | 0.81 | 0.88 | 74 | MG, AGS |
Interfaces
6 interfaces between chains.
- A–F · 3764 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3755 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 3750 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3749 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 3743 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 7JY5 · Structure of human p97 in complex with ATPgammaS and Npl4/Ufd1 (masked around p97) · 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 7JY5 · PDBe 7JY5 · UniProt P55072
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