Research workbench
Crystal structure of triosephosphate isomerase from thermoplasma acidophilum with glycerol 3-phosphate
Analyse Crystal structure of triosephosphate isomerase from thermoplasma acidophilum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CSS
- Type
- protein
- Length
- 856 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
- G3P, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Triosephosphate isomerase (EC 5.3.1.1) | protein | 214 | 41% helix, 20% strand | Q9HLB6 |
Ligands and binding sites
- G3P · Sn-glycerol-3-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.81 | 0.82 | 100 | empty |
| 2 | 141 | 0.40 | 0.74 | 30 | empty |
| 3 | 90 | 0.35 | 0.74 | 15 | empty |
| 4 | 77 | 0.33 | 0.74 | 13 | empty |
| 5 | 64 | 0.29 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1541 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1537 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 270 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q9HLB6 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (Q9HLB6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5CSS · PDBe 5CSS · UniProt Q9HLB6
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