MolNFT v1 · #84135 · protein
Electrophilic catalysis in triosephosphase isomerase: the role of histidine-95
3YPI · Triosephosphate isomerase: “Electrophilic catalysis in triosephosphase isomerase: the role of histidine-95”. X-ray diffraction, 1 ligand (PGH), 5 pockets (best druggability 0.63). MolNFT v1 #84135 on GenesisL1: 3D structure, binding…
- PDB
- 3YPI
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- UniProt
- P00942
- Ligands
- PGH
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 247 | 43% helix, 17% strand | P00942 |
Ligands and binding sites
- PGH · Phosphoglycolohydroxamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.63 | 0.92 | 25 | empty |
| 2 | 70 | 0.46 | 0.83 | 23 | PGH |
| 3 | 68 | 0.45 | 0.82 | 19 | PGH |
| 4 | 55 | 0.33 | 0.78 | 18 | empty |
| 5 | 53 | 0.29 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1681 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3YPI · Electrophilic catalysis in triosephosphase isomerase: the role of histidine-95 · the same entry in another collection · chain A against A, TM-score 1.00
- P00942 · AlphaFold monomer V2.0 prediction for triosephosphate isomerase (P00942) · 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 P00942
- Elsewhere: RCSB PDB 3YPI · PDBe 3YPI · UniProt P00942
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