Research workbench
Crystal structures of trehalose synthase from deinococcus radiodurans reveal that a closed conformation is involved in the intramolecular isomerization catalysis
Analyse Crystal structures of trehalose synthase from deinococcus radiodurans reveal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WF7
- Type
- protein
- Length
- 2,192 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose synthase
- EC
- 5.4.99.16
- UniProt
- I3NX86
- Ligands
- CA, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Trehalose synthase (EC 5.4.99.16) | protein | 548 | 32% helix, 18% strand | I3NX86 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.86 | 0.93 | 54 | empty |
| 2 | 1117 | 0.84 | 0.85 | 112 | empty |
| 3 | 184 | 0.82 | 0.96 | 36 | TRS |
| 4 | 157 | 0.80 | 0.97 | 33 | TRS |
| 5 | 172 | 0.80 | 0.96 | 34 | TRS |
Interfaces
6 interfaces between chains.
- B–C · 1568 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 1542 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 332 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WF7 · Crystal structures of trehalose synthase from Deinococcus radiodurans reveal that a… · 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 I3NX86
- Elsewhere: RCSB PDB 4WF7 · PDBe 4WF7 · UniProt I3NX86
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