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The crystal structure of candida glabrata THI6, a bifunctional enzyme involved in thiamin biosyhthesis of eukaryotes
Analyse The crystal structure of candida glabrata THI6, a bifunctional enzyme involved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NM1
- Type
- protein
- Length
- 3,040 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine biosynthetic bifunctional enzyme
- EC
- 2.5.1.3, 2.7.1.50
- UniProt
- Q6FV03
- Ligands
- 3NM, IFP, POP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 507 | 43% helix, 15% strand | Q6FV03 |
| E | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 505 | 42% helix, 16% strand | Q6FV03 |
Ligands and binding sites
- 3NM · 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid · ligand · 6 copies · chains A, F, E, D, C, B
- IFP · 2-trifluoromethyl-5-methylene-5H-pyrimidin-4-ylideneamine · ligand · 6 copies · chains A, F, E, D, C, B
- POP · Pyrophosphate 2- · ligand · 6 copies · chains A, F, E, D, C, B
- MG · Magnesium ion · metal · 6 copies · chains A, F, E, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.83 | 0.84 | 124 | empty |
| 2 | 861 | 0.82 | 0.84 | 139 | empty |
| 3 | 192 | 0.79 | 0.94 | 21 | empty |
| 4 | 599 | 0.77 | 0.83 | 65 | 3NM, IFP, POP, MG |
| 5 | 607 | 0.75 | 0.82 | 66 | 3NM, IFP, POP, MG |
Interfaces
9 interfaces between chains.
- A–E · 819 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 805 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 803 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 725 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3NM1 · The Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin… · the same entry in another collection · chain B against B, 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 Q6FV03
- Elsewhere: RCSB PDB 3NM1 · PDBe 3NM1 · UniProt Q6FV03
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