MolNFT v1 · #110848 · protein
Crystal structure of triosephosphate isomerase from deinococcus radiodurans
4Y90: “Crystal structure of triosephosphate isomerase from deinococcus radiodurans”. X-ray diffraction, 3 ligands (CA, NA, SO4), 9 pockets (best druggability 0.71). MolNFT v1 #110848 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4Y90
- Type
- protein
- Length
- 976 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q9RUP5
- Ligands
- CA, NA, SO4
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 244 | 47% helix, 17% strand | Q9RUP5 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.71 | 0.87 | 44 | GOL, CA |
| 2 | 247 | 0.70 | 0.86 | 46 | GOL |
| 3 | 390 | 0.57 | 0.75 | 59 | empty |
| 4 | 298 | 0.53 | 0.75 | 45 | empty |
| 5 | 65 | 0.37 | 0.79 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1565 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 130 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Y90 · Crystal structure of Triosephosphate Isomerase from Deinococcus radiodurans · 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 Q9RUP5
- Elsewhere: RCSB PDB 4Y90 · PDBe 4Y90 · UniProt Q9RUP5
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