MolNFT v1 · #140736 · protein
The N253F mutant structure of trehalose synthase from deinococcus radiodurans reveals an open active-site conformation
5YKB: “The N253F mutant structure of trehalose synthase from deinococcus radiodurans reveals an open active-site…”. X-ray diffraction, 2 ligands (CA, MG), 20 pockets (best druggability 0.86). MolNFT v1 #140736 on GenesisL1: 3D structure…
- PDB
- 5YKB
- Type
- protein
- Length
- 2,104 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 · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trehalose synthase (EC 5.4.99.16) | protein | 529 | 33% helix, 19% strand | I3NX86 |
| B | Trehalose synthase (EC 5.4.99.16) | protein | 522 | 34% helix, 19% strand | I3NX86 |
| C | Trehalose synthase (EC 5.4.99.16) | protein | 530 | 32% helix, 20% strand | I3NX86 |
| D | Trehalose synthase (EC 5.4.99.16) | protein | 523 | 33% helix, 19% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.86 | 0.87 | 108 | empty |
| 2 | 1089 | 0.86 | 0.87 | 112 | empty |
| 3 | 908 | 0.80 | 0.82 | 71 | empty |
| 4 | 372 | 0.70 | 0.82 | 36 | empty |
| 5 | 377 | 0.69 | 0.81 | 38 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1566 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1563 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 476 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 294 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 72 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5YKB · The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an… · the same entry in another collection · chain B against B, 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 5YKB · PDBe 5YKB · UniProt I3NX86
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