Research workbench
P97 D1D2 with CB5083 bound
Analyse P97 D1D2 with CB5083 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MCK
- Type
- protein
- Length
- 6,108 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transitional endoplasmic reticulum ATPase
- EC
- 3.6.4.6
- UniProt
- P55072
- Ligands
- JDP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 509 | 54% helix, 11% strand | P55072 |
Ligands and binding sites
- JDP · 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide · 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 | 945 | 0.83 | 0.84 | 100 | empty |
| 2 | 965 | 0.82 | 0.84 | 102 | empty |
| 3 | 906 | 0.82 | 0.84 | 109 | empty |
| 4 | 907 | 0.82 | 0.84 | 105 | empty |
| 5 | 837 | 0.82 | 0.85 | 92 | empty |
Interfaces
24 interfaces between chains.
- J–K · 3015 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 3011 Ų buried · 32 hydrogen bonds · protein-protein
- A–F · 2991 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2984 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2976 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6MCK · p97 D1D2 with CB5083 bound · 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 6MCK · PDBe 6MCK · UniProt P55072
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