MolNFT v1 · #115744 · protein
Crystal structure of triosephosphate isomerase from thermoplasma acidophilium
5CSR: “Crystal structure of triosephosphate isomerase from thermoplasma acidophilium”. X-ray diffraction, 1 ligand (CL), 10 pockets (best druggability 0.79). MolNFT v1 #115744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CSR
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- Q9HLB6
- Ligands
- CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 215 | 42% helix, 19% strand | Q9HLB6 |
| C, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 220 | 39% helix, 19% strand | Q9HLB6 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.79 | 0.81 | 105 | empty |
| 2 | 234 | 0.55 | 0.78 | 25 | empty |
| 3 | 241 | 0.53 | 0.76 | 25 | empty |
| 4 | 195 | 0.50 | 0.76 | 27 | empty |
| 5 | 162 | 0.47 | 0.76 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1547 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1537 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 394 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 392 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CSR · Crystal structure of triosephosphate isomerase from Thermoplasma acidophilium · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HLB6 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q9HLB6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9HLB6
- Elsewhere: RCSB PDB 5CSR · PDBe 5CSR · UniProt Q9HLB6
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