Research workbench
Crystal structure of a putative glycosidase (TM1410) from thermotoga maritima at 2.20 a resolution
Analyse Crystal structure of a putative glycosidase (TM1410) from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AAM
- Type
- protein
- Length
- 1,717 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TM1410
- UniProt
- Q9X1D0
- Ligands
- UNL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein TM1410 | protein | 285 | 39% helix, 24% strand | Q9X1D0 |
| B, E | Hypothetical protein TM1410 | protein | 287 | 38% helix, 23% strand | Q9X1D0 |
| C, D, F | Hypothetical protein TM1410 | protein | 286 | 38% helix, 24% strand | Q9X1D0 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 37 copies · chains A, D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.76 | 0.78 | 75 | empty |
| 2 | 1127 | 0.73 | 0.76 | 89 | empty |
| 3 | 313 | 0.61 | 0.79 | 38 | UNL, GOL |
| 4 | 358 | 0.61 | 0.77 | 41 | UNL, GOL |
| 5 | 301 | 0.60 | 0.78 | 40 | UNL, GOL |
Interfaces
7 interfaces between chains.
- A–D · 492 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 474 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 473 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 462 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 427 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 2AAM · Crystal structure of a putative glycosidase (tm1410) from thermotoga maritima at 2.20 A… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9X1D0 · AlphaFold monomer V2.0 prediction for uncharacterized protein TM_1410 (Q9X1D0) · a predicted model of the same protein · 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 Q9X1D0
- Elsewhere: RCSB PDB 2AAM · PDBe 2AAM · UniProt Q9X1D0
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