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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
- 3NL5
- Type
- protein
- Length
- 1,533 residues
- Chains
- 3
- 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
- ACP, TZE, MG
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 512 | 42% helix, 15% strand | Q6FV03 |
| B | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 510 | 40% helix, 15% strand | Q6FV03 |
| C | Thiamine biosynthetic bifunctional enzyme (EC 2.5.1.3, 2.7.1.50) | protein | 511 | 42% helix, 15% strand | Q6FV03 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 3 copies · chains A, B, C
- TZE · 2-(4-methyl-thiazol-5-yl)-ethanol · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.82 | 0.86 | 96 | empty |
| 2 | 584 | 0.72 | 0.80 | 56 | MG, ACP, TZE |
| 3 | 597 | 0.71 | 0.79 | 53 | MG, ACP, TZE |
| 4 | 572 | 0.70 | 0.79 | 50 | MG, ACP, TZE |
| 5 | 79 | 0.45 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 845 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 836 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3NL5 · 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 3NL5 · PDBe 3NL5 · UniProt Q6FV03
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