Research workbench
Yeast lon (PIM1) with endogenous substrate
Analyse Yeast lon (PIM1) with endogenous substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SXO
- Type
- protein
- Length
- 3,169 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lon protease homolog, mitochondrial; Endogenous substrate
- EC
- 3.4.21.53
- UniProt
- P36775
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 544 | 43% helix, 14% strand | P36775 |
| B | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 487 | 38% helix, 13% strand | P36775 |
| C | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 487 | 38% helix, 14% strand | P36775 |
| D | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 547 | 41% helix, 14% strand | P36775 |
| E | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 546 | 43% helix, 13% strand | P36775 |
| F | Lon protease homolog, mitochondrial (EC 3.4.21.53) | protein | 549 | 37% helix, 13% strand | P36775 |
| G | Endogenous substrate | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, F, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, F, 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 | 689 | 0.86 | 0.90 | 108 | ADP |
| 2 | 522 | 0.85 | 0.91 | 73 | empty |
| 3 | 373 | 0.82 | 0.91 | 50 | empty |
| 4 | 552 | 0.80 | 0.86 | 89 | MG |
| 5 | 484 | 0.79 | 0.87 | 60 | ATP |
Interfaces
16 interfaces between chains.
- E–F · 3308 Ų buried · 49 hydrogen bonds · protein-protein
- D–E · 3231 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 3204 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2472 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2394 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
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 P36775
- Elsewhere: RCSB PDB 7SXO · PDBe 7SXO · UniProt P36775
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