Research workbench
Crystal structure of amylosucrase from calidithermus timidus
Analyse Crystal structure of amylosucrase from calidithermus timidus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ESH
- Type
- protein
- Length
- 2,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amylosucrase
- EC
- 2.4.1.4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Amylosucrase (EC 2.4.1.4) | protein | 646 | 44% helix, 16% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.85 | 0.92 | 62 | empty |
| 2 | 1044 | 0.83 | 0.84 | 93 | empty |
| 3 | 534 | 0.76 | 0.83 | 64 | TRS |
| 4 | 546 | 0.75 | 0.83 | 61 | TRS |
| 5 | 542 | 0.75 | 0.82 | 53 | TRS |
Interfaces
4 interfaces between chains.
- C–D · 1292 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1255 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 669 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7ESH · Crystal structure of amylosucrase from Calidithermus timidus · 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
- Elsewhere: RCSB PDB 7ESH · PDBe 7ESH
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