Research workbench
Correction of X-ray intensities from an hslv-hslu co- crystal containing lattice translocation defects
Analyse Correction of X-ray intensities from an hslv-hslu co- crystal containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYF
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent hsl protease ATP-binding subunit hslu; ATP-dependent protease hslv
- EC
- 3.4.25.-
- UniProt
- P0A6H5, P39070
- Ligands
- ADP
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-dependent hsl protease ATP-binding subunit hslu | protein | 408 | 43% helix, 10% strand | P0A6H5 |
| D, C | ATP-dependent protease hslv (EC 3.4.25.-) | protein | 180 | 33% helix, 27% strand | P39070 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.85 | 0.86 | 96 | ADP |
| 2 | 1160 | 0.81 | 0.82 | 101 | empty |
| 3 | 50 | 0.72 | 0.99 | 20 | empty |
| 4 | 389 | 0.59 | 0.75 | 52 | empty |
| 5 | 213 | 0.58 | 0.80 | 27 | ADP |
Interfaces
4 interfaces between chains.
- A–B · 2151 Ų buried · 22 hydrogen bonds · protein-protein
- D–C · 920 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 459 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1YYF · Correction of X-ray Intensities from an HslV-HslU co-crystal containing lattice… · the same entry in another collection · chain A against A, TM-score 1.00
- P39070 · AlphaFold monomer V2.0 prediction for ATP-dependent protease subunit clpq (P39070) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P0A6H5 · AlphaFold monomer V2.0 prediction for ATP-dependent protease ATPase subunit hslu (P0A6H5) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P0A6H5
- Every structure of UniProt P39070
- Elsewhere: RCSB PDB 1YYF · PDBe 1YYF · UniProt P0A6H5 · UniProt P39070
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