Research workbench
Cryo-EM structure of human P97 in complex with nms-873 in the presence of ATP, NPL4/UFD1, and UB6
Analyse Cryo-EM structure of human P97 in complex with nms-873 in the presence of ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LMY
- Type
- protein
- Length
- 4,470 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
- ATP, Y6Y, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 44% 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 | 745 | 44% helix, 17% strand | P55072 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, F, B, C, D, E
- Y6Y · 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine · ligand · 6 copies · chains A, B, C, D, E, F
- 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 | 801 | 0.84 | 0.87 | 105 | ATP, MG |
| 2 | 781 | 0.84 | 0.87 | 108 | ATP, MG |
| 3 | 760 | 0.84 | 0.87 | 111 | ATP, MG |
| 4 | 762 | 0.83 | 0.87 | 95 | ATP, MG |
| 5 | 559 | 0.81 | 0.87 | 79 | ATP, MG |
Interfaces
6 interfaces between chains.
- A–F · 3912 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 3891 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 3886 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3882 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 3873 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 7LMY · Cryo-EM structure of human p97 in complex with NMS-873 in the presence of ATP, Npl4/Ufd1… · 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 7LMY · PDBe 7LMY · UniProt P55072
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