MolNFT v1 · #38084 · protein
Tena HOMOLOG/THI-4 thiaminase complexed with product 4-amino-5- hydroxymethyl-2-methylpyrimidine
2GM8: “Tena HOMOLOG/THI-4 thiaminase complexed with product 4-amino-5- hydroxymethyl-2-methylpyrimidine”. X-ray diffraction, 1 ligand (HMH), 5 pockets (best druggability 0.76). MolNFT v1 #38084 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2GM8
- Type
- protein
- Length
- 862 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
- HMH
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tena HOMOLOG/THI-4 thiaminase (EC 2.5.1.2) | protein | 217 | 82% helix, 0% strand | Q8ZZM9 |
| B | Tena HOMOLOG/THI-4 thiaminase (EC 2.5.1.2) | protein | 213 | 83% helix, 0% strand | Q8ZZM9 |
| C | Tena HOMOLOG/THI-4 thiaminase (EC 2.5.1.2) | protein | 215 | 83% helix, 0% strand | Q8ZZM9 |
Ligands and binding sites
- HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.76 | 0.97 | 22 | empty |
| 2 | 948 | 0.74 | 0.77 | 79 | empty |
| 3 | 905 | 0.73 | 0.77 | 78 | empty |
| 4 | 71 | 0.34 | 0.76 | 15 | EDO |
| 5 | 71 | 0.34 | 0.75 | 15 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 902 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 870 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 748 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 740 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 148 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GM8 · TenA Homolog/Thi-4 Thiaminase complexed with product… · the same entry in another collection · chain C against C, 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 2GM8 · PDBe 2GM8 · UniProt Q8ZZM9
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