Research workbench
Helical structure of BcThsA in complex with 1''-3'gcADPR
Analyse Helical structure of BcThsA in complex with 1''-3'gcADPR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8BTO
- Type
- protein
- Length
- 5,676 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.96
- Source
- Bacillus cereus MSX-D12
- Molecule
- NAD(+) hydrolase ThsA
- EC
- 3.2.2.5
- UniProt
- J8G6Z1
- Ligands
- OJC, NAD
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 2.96 · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | NAD(+) hydrolase ThsA (EC 3.2.2.5) | protein | 473 | 53% helix, 14% strand | J8G6Z1 |
Ligands and binding sites
- OJC · (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.83 | 0.85 | 89 | empty |
| 2 | 941 | 0.83 | 0.84 | 98 | empty |
| 3 | 822 | 0.81 | 0.83 | 70 | NAD |
| 4 | 839 | 0.81 | 0.83 | 79 | empty |
| 5 | 601 | 0.81 | 0.86 | 73 | empty |
Interfaces
28 interfaces between chains.
- G–H · 2192 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2185 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 2183 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 2182 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2180 Ų buried · 20 hydrogen bonds · protein-protein
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 J8G6Z1
- Elsewhere: RCSB PDB 8BTO · PDBe 8BTO · UniProt J8G6Z1
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