Research workbench
Cryo-EM structure of dodecamer P97
Analyse Cryo-EM structure of dodecamer P97 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WUB
- Type
- protein
- Length
- 7,985 residues
- Chains
- 12
- 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, Y6Y
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 576 | 48% helix, 9% strand | P55072 |
| C | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 576 | 48% helix, 9% strand | P55072 |
| D | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 575 | 48% helix, 9% strand | P55072 |
| G, H, I, J, K, L | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 755 | 38% helix, 15% strand | P55072 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- Y6Y · 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
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 | 1101 | 0.85 | 0.86 | 133 | ADP |
| 2 | 1068 | 0.84 | 0.85 | 141 | ADP |
| 3 | 825 | 0.83 | 0.86 | 108 | empty |
| 4 | 935 | 0.83 | 0.85 | 130 | ADP |
| 5 | 763 | 0.82 | 0.85 | 98 | empty |
Interfaces
24 interfaces between chains.
- I–J · 4058 Ų buried · 45 hydrogen bonds · protein-protein
- J–K · 4055 Ų buried · 46 hydrogen bonds · protein-protein
- K–L · 4051 Ų buried · 45 hydrogen bonds · protein-protein
- G–L · 4035 Ų buried · 42 hydrogen bonds · protein-protein
- G–H · 4031 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 7WUB · Cryo-EM structure of dodecamer 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 7WUB · PDBe 7WUB · UniProt P55072
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