MolNFT v1 · #38083 · protein
Tena HOMOLOG/THI-4 thiaminase from pyrobaculum aerophilum
2GM7: “Tena HOMOLOG/THI-4 thiaminase from pyrobaculum aerophilum”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.74). MolNFT v1 #38083 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GM7
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tena HOMOLOG/THI-4 thiaminase
- EC
- 2.5.1.2
- UniProt
- Q8ZZM9
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tena HOMOLOG/THI-4 thiaminase (EC 2.5.1.2) | protein | 212 | 85% helix, 0% strand | Q8ZZM9 |
| D | Tena HOMOLOG/THI-4 thiaminase (EC 2.5.1.2) | protein | 216 | 83% helix, 0% strand | Q8ZZM9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.74 | 0.77 | 83 | empty |
| 2 | 260 | 0.74 | 0.87 | 27 | PE4 |
| 3 | 911 | 0.73 | 0.77 | 78 | empty |
| 4 | 273 | 0.72 | 0.86 | 27 | PE4 |
| 5 | 57 | 0.72 | 0.99 | 24 | GOL |
Interfaces
6 interfaces between chains.
- A–B · 891 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 872 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 733 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GM7 · TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum · 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
- Every structure of UniProt Q8ZZM9
- Elsewhere: RCSB PDB 2GM7 · PDBe 2GM7 · UniProt Q8ZZM9
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