Research workbench
Cryo-EM structure of human P97 bound to cb-5083 and atpgs.
Analyse Cryo-EM structure of human P97 bound to cb-5083 and atpgs. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RLJ
- Type
- protein
- Length
- 8,736 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
- AGS, JDP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 34% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, L, G, H, I, J, K | Transitional endoplasmic reticulum ATPase (EC 3.6.4.6) | protein | 728 | 34% helix, 12% strand | P55072 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains A, F, B, C, D, E, L, K, G, H, I, J
- 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, L, G, H, I, J, K
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F, L, G, H, I, J, K
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 | 1027 | 0.86 | 0.87 | 125 | empty |
| 2 | 705 | 0.85 | 0.89 | 105 | empty |
| 3 | 1177 | 0.85 | 0.86 | 131 | AGS, MG |
| 4 | 736 | 0.85 | 0.88 | 106 | empty |
| 5 | 1053 | 0.85 | 0.86 | 123 | empty |
Interfaces
24 interfaces between chains.
- L–G · 3681 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 3626 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 3622 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 3611 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3558 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7RLJ · Cryo-EM structure of human p97 bound to CB-5083 and ATPgS. · the same entry in another collection · chain J against J, 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 7RLJ · PDBe 7RLJ · UniProt P55072
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