MolNFT v1 · #145226 · protein
CDC48-NPL4 complex in the presence of ATP-gamma-S
6CHS: “CDC48-NPL4 complex in the presence of ATP-gamma-S”. Electron microscopy, 3 ligands (AGS, MG, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #145226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CHS
- Type
- protein
- Length
- 3,760 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NPL4; Putative cell division control protein
- UniProt
- G0S0B4, G0S6Y2
- Ligands
- AGS, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NPL4 | protein | 460 | 25% helix, 18% strand | G0S0B4 |
| H, I, J, D, E, F | Putative cell division control protein | protein | 550 | 48% helix, 10% strand | G0S6Y2 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 12 copies · chains H, F, I, J, D, E
- MG · Magnesium ion · metal · 12 copies · chains H, I, J, D, E, F
- ZN · Zinc ion · metal · 2 copies · chains A
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 | 751 | 0.83 | 0.86 | 111 | AGS, MG |
| 2 | 1034 | 0.83 | 0.84 | 109 | empty |
| 3 | 712 | 0.83 | 0.87 | 106 | AGS, MG |
| 4 | 1073 | 0.82 | 0.83 | 118 | AGS, MG |
| 5 | 640 | 0.82 | 0.87 | 91 | empty |
Interfaces
12 interfaces between chains.
- H–I · 3510 Ų buried · 32 hydrogen bonds · protein-protein
- J–D · 3503 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 3501 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 3469 Ų buried · 35 hydrogen bonds · protein-protein
- H–F · 3325 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6CHS · Cdc48-Npl4 complex in the presence of ATP-gamma-S · 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 G0S0B4
- Every structure of UniProt G0S6Y2
- Elsewhere: RCSB PDB 6CHS · PDBe 6CHS · UniProt G0S0B4 · UniProt G0S6Y2
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