Research workbench
Crystal structure of Rv3378c_Y51F with TPP
Analyse Crystal structure of Rv3378c_Y51F with TPP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WQN
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Mycobacterium tuberculosis
- Molecule
- Diterpene synthase
- EC
- 3.1.7.9, 3.1.7.8
- UniProt
- O50407
- Ligands
- 9AX, PO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diterpene synthase (EC 3.1.7.9, 3.1.7.8) | protein | 292 | 48% helix, 14% strand | O50407 |
Ligands and binding sites
- 9AX · (2E)-3-methyl-5-[(1R,2S,8aS)-1,2,5,5-tetramethyl-1,2,3,5,6,7,8,8a-octahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.75 | 0.82 | 50 | 9AX |
| 2 | 113 | 0.43 | 0.77 | 24 | empty |
Compared structures
- 3WQN · Crystal structure of RV3378C_Y51F with tpp · 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 O50407
- Elsewhere: RCSB PDB 3WQN · PDBe 3WQN · UniProt O50407
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