Research workbench
Structure of the wild-type C3BOT1 exoenzyme (nicotinamide- bound state, crystal form I)
Analyse Structure of the wild-type C3BOT1 exoenzyme (nicotinamide- bound state, crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C8A
- Type
- protein
- Length
- 819 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mono-ADP-ribosyltransferase C3
- EC
- 2.4.2.-
- UniProt
- P15879
- Ligands
- NCA, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 208 | 36% helix, 25% strand | P15879 |
| B | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 202 | 33% helix, 25% strand | P15879 |
| C | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 207 | 34% helix, 26% strand | P15879 |
| D | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 202 | 33% helix, 25% strand | P15879 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.76 | 0.83 | 47 | NCA, SO4 |
| 2 | 698 | 0.74 | 0.80 | 68 | empty |
| 3 | 166 | 0.58 | 0.82 | 34 | NCA, SO4 |
| 4 | 202 | 0.58 | 0.81 | 37 | NCA, SO4 |
| 5 | 184 | 0.54 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–D · 543 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 424 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 377 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 310 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 218 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2C8A · Structure of the wild-type C3bot1 Exoenzyme (Nicotinamide-bound state, crystal form I) · 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 P15879
- Elsewhere: RCSB PDB 2C8A · PDBe 2C8A · UniProt P15879
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