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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
- 3NM3
- Type
- protein
- Length
- 3,053 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
- TPS, POP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 510 | 43% helix, 15% strand | Q6FV03 |
| B | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 508 | 44% helix, 16% strand | Q6FV03 |
| C | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 510 | 44% helix, 16% strand | Q6FV03 |
| D | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 511 | 42% helix, 15% strand | Q6FV03 |
| E, F | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 507 | 43% helix, 16% strand | Q6FV03 |
Ligands and binding sites
- TPS · Thiamin phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- POP · Pyrophosphate 2- · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.79 | 0.81 | 94 | empty |
| 2 | 1110 | 0.79 | 0.80 | 120 | empty |
| 3 | 819 | 0.78 | 0.81 | 97 | MG, TPS, POP |
| 4 | 1165 | 0.76 | 0.78 | 115 | empty |
| 5 | 631 | 0.73 | 0.80 | 65 | MG, TPS, POP |
Interfaces
9 interfaces between chains.
- D–E · 847 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 804 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 722 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 720 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3NM3 · The Crystal Structure of Candida glabrata THI6, a Bifunctional Enzyme involved in Thiamin… · 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 Q6FV03
- Elsewhere: RCSB PDB 3NM3 · PDBe 3NM3 · UniProt Q6FV03
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