Research workbench
Structure of P97/VCP in complex with ADP/AMP-pnp
Analyse Structure of P97/VCP in complex with ADP/AMP-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CF2
- Type
- protein
- Length
- 2,636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- UniProt
- Q01853
- Ligands
- ADP, ANP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transitional endoplasmic reticulum ATPase | protein | 659 | 34% helix, 16% strand | Q01853 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, B, C, D
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 | 1190 | 0.84 | 0.85 | 141 | ADP |
| 2 | 646 | 0.83 | 0.87 | 102 | empty |
| 3 | 575 | 0.74 | 0.82 | 61 | empty |
| 4 | 566 | 0.74 | 0.81 | 60 | empty |
| 5 | 59 | 0.73 | 0.98 | 21 | empty |
Interfaces
2 interfaces between chains.
- C–D · 3403 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3392 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3CF2 · Structure of P97/vcp in complex with ADP/AMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q01853 · AlphaFold monomer V2.0 prediction for transitional endoplasmic reticulum ATPase (Q01853) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 Q01853
- Elsewhere: RCSB PDB 3CF2 · PDBe 3CF2 · UniProt Q01853
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