MolNFT v1 · #121712 · protein
Structure-function studies on role of hydrophobic clamping of a basic glutamate in catalysis by triosephosphate isomerase
5I3I · Triosephosphate isomerase, glycosomal: “Structure-function studies on role of hydrophobic clamping of a basic glutamate in catalysis by…”. X-ray diffraction, 1 ligand (PGA), 8 pockets (best druggability 0.66). MolNFT v1 #121712 on…
- PDB
- 5I3I
- Type
- protein
- Length
- 996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase, glycosomal
- EC
- 5.3.1.1
- UniProt
- P04789
- Ligands
- PGA
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Triosephosphate isomerase, glycosomal (EC 5.3.1.1) | protein | 249 | 46% helix, 17% strand | P04789 |
Ligands and binding sites
- PGA · 2-phosphoglycolic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.66 | 0.77 | 79 | PGA |
| 2 | 192 | 0.46 | 0.74 | 30 | empty |
| 3 | 68 | 0.43 | 0.81 | 27 | PGA |
| 4 | 65 | 0.41 | 0.81 | 25 | PGA |
| 5 | 130 | 0.35 | 0.72 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1586 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1568 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 70 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5I3I · Structure-Function Studies on Role of Hydrophobic Clamping of a Basic Glutamate in… · the same entry in another collection · chain B against B, TM-score 1.00
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain B against A, TM-score 0.98
- 4TIM · Crystallographic and molecular modeling studies on trypanosomal triosephosphate… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P04789
- Elsewhere: RCSB PDB 5I3I · PDBe 5I3I · UniProt P04789
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