MolNFT v1 · #157908 · protein
Crystal structure of a reconstructed ancestor of triosephosphate isomerase from eukaryotes
6NEE: “Crystal structure of a reconstructed ancestor of triosephosphate isomerase from eukaryotes”. X-ray diffraction, 1 ligand (PGH), 3 pockets (best druggability 0.75). MolNFT v1 #157908 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NEE
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Triosephosphate isomerase
- EC
- 5.3.1.1
- Ligands
- PGH
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Triosephosphate isomerase (EC 5.3.1.1) | protein | 250 | 44% helix, 17% strand | — |
| B | Triosephosphate isomerase (EC 5.3.1.1) | protein | 252 | 44% helix, 17% strand | — |
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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.75 | 0.96 | 30 | empty |
| 2 | 60 | 0.38 | 0.80 | 25 | PGH |
| 3 | 55 | 0.33 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1664 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6NEE · Crystal structure of a reconstructed ancestor of Triosephosphate isomerase from eukaryotes · 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
- Elsewhere: RCSB PDB 6NEE · PDBe 6NEE
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