Research workbench
Crystal structure of an isatin hydrolase bound to product analogue thioisatinate
Analyse Crystal structure of an isatin hydrolase bound to product analogue thioisatinate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M8D
- Type
- protein
- Length
- 3,147 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- A0NLY7
- Ligands
- 23J, CA, MN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, J, K, L | Putative uncharacterized protein | protein | 262 | 28% helix, 27% strand | A0NLY7 |
| B | Putative uncharacterized protein | protein | 262 | 27% helix, 27% strand | A0NLY7 |
| D, F, H | Putative uncharacterized protein | protein | 263 | 28% helix, 27% strand | A0NLY7 |
Ligands and binding sites
- 23J · oxo(2-sulfanylphenyl)acetic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CA · Calcium ion · metal · 16 copies · chains A, B, K, C, D, F, I, J, L
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.83 | 0.84 | 126 | 23J, MN, CA |
| 2 | 1105 | 0.81 | 0.82 | 102 | CA |
| 3 | 966 | 0.80 | 0.81 | 97 | 23J, CA |
| 4 | 183 | 0.72 | 0.89 | 37 | MN, 23J |
| 5 | 191 | 0.72 | 0.88 | 36 | MN, 23J |
Interfaces
22 interfaces between chains.
- I–J · 3915 Ų buried · 56 hydrogen bonds · protein-protein
- E–F · 3903 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 3871 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3868 Ų buried · 55 hydrogen bonds · protein-protein
- K–L · 3859 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 4M8D · Crystal structure of an isatin hydrolase bound to product analogue thioisatinate · the same entry in another collection · chain J against J, 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 A0NLY7
- Elsewhere: RCSB PDB 4M8D · PDBe 4M8D · UniProt A0NLY7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.