Research workbench
Crystal structure analysis of clpsn heterodimer
Analyse Crystal structure analysis of clpsn heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MBU
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent clp protease ATP-binding subunit clp a; Protein ylja
- UniProt
- P0ABH9, P0A8Q6
- Ligands
- YBT, CL
- Pockets
- 4 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent clp protease ATP-binding subunit clp a | protein | 142 | 63% helix, 6% strand | P0ABH9 |
| C, D | Protein ylja | protein | 86 | 50% helix, 24% strand | P0A8Q6 |
Ligands and binding sites
- YBT · Bis-(2-hydroxyethyl)amino-tris(hydroxymethyl)methane yttrium · ligand · 4 copies · chains A, B, D
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.42 | 0.78 | 21 | empty |
| 2 | 54 | 0.39 | 0.81 | 14 | empty |
| 3 | 50 | 0.37 | 0.80 | 12 | empty |
| 4 | 64 | 0.28 | 0.72 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 874 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 861 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 506 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1MBU · Crystal Structure Analysis of ClpSN heterodimer · the same entry in another collection · chain D against D, TM-score 1.00
- P0ABH9 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease ATP- binding subunit… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P0A8Q6 · AlphaFold monomer V2.0 prediction for ATP-dependent clp protease adapter protein clps… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P0ABH9
- Every structure of UniProt P0A8Q6
- Elsewhere: RCSB PDB 1MBU · PDBe 1MBU · UniProt P0ABH9 · UniProt P0A8Q6
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