Research workbench
Crystal structure of amidohydrolase from thermotoga maritima MSB8
Analyse Crystal structure of amidohydrolase from thermotoga maritima MSB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OOQ
- Type
- protein
- Length
- 3,835 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase
- UniProt
- Q9X247
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Amidohydrolase | protein | 384 | 33% helix, 25% strand | Q9X247 |
| B, E, G, H, I, J | Amidohydrolase | protein | 383 | 33% helix, 25% strand | Q9X247 |
| F | Amidohydrolase | protein | 385 | 32% helix, 25% strand | Q9X247 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, E, I, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.79 | 0.84 | 95 | empty |
| 2 | 551 | 0.78 | 0.85 | 71 | empty |
| 3 | 589 | 0.77 | 0.84 | 90 | empty |
| 4 | 470 | 0.76 | 0.84 | 67 | empty |
| 5 | 490 | 0.76 | 0.84 | 66 | empty |
Interfaces
24 interfaces between chains.
- H–J · 1646 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1642 Ų buried · 20 hydrogen bonds · protein-protein
- C–J · 1626 Ų buried · 18 hydrogen bonds · protein-protein
- E–I · 1610 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1598 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 110 modified (engineered).
Compared structures
- 3OOQ · CRYSTAL STRUCTURE OF amidohydrolase from Thermotoga maritima MSB8 · 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 Q9X247
- Elsewhere: RCSB PDB 3OOQ · PDBe 3OOQ · UniProt Q9X247
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