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Structure of the clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD
Analyse Structure of the clostridium botulinum C3 exoenzyme (wild-type) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GZF
- Type
- protein
- Length
- 825 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
- NAD, ADP, NIR, SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 203 | 37% helix, 25% strand | P15879 |
| B | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 211 | 35% helix, 26% strand | P15879 |
| C | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 208 | 34% helix, 26% strand | P15879 |
| D | Mono-ADP-ribosyltransferase C3 (EC 2.4.2.-) | protein | 203 | 36% helix, 25% strand | P15879 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D
- NIR · 3-(aminocarbonyl)-1-[(3R,4S,5R)-3,4-dihydroxy-5-methyltetrahydro-2-furanyl]pyridinium · ligand · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.78 | 0.86 | 56 | NAD |
| 2 | 530 | 0.75 | 0.83 | 65 | empty |
| 3 | 201 | 0.55 | 0.79 | 36 | NIR, ADP |
| 4 | 187 | 0.55 | 0.79 | 23 | empty |
| 5 | 213 | 0.55 | 0.78 | 34 | NAD |
Interfaces
6 interfaces between chains.
- A–C · 545 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 329 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 293 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1GZF · Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD · 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 1GZF · PDBe 1GZF · UniProt P15879
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