Research workbench
Structure of carbapenem synthase (carc) complexed with N-acetyl proline
Analyse Structure of carbapenem synthase (carc) complexed with N-acetyl proline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NX8
- Type
- protein
- Length
- 750 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem synthase
- UniProt
- Q9XB59
- Ligands
- AKG, N7P, FE
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem synthase | protein | 248 | 23% helix, 30% strand | Q9XB59 |
| B | Carbapenem synthase | protein | 256 | 24% helix, 29% strand | Q9XB59 |
| C | Carbapenem synthase | protein | 246 | 23% helix, 30% strand | Q9XB59 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- N7P · 1-acetyl-L-proline · ligand · 2 copies · chains B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.66 | 0.85 | 31 | FE, AKG |
| 2 | 192 | 0.63 | 0.83 | 31 | FE, AKG, N7P |
| 3 | 281 | 0.61 | 0.79 | 38 | AKG, N7P |
| 4 | 320 | 0.59 | 0.77 | 52 | empty |
| 5 | 237 | 0.55 | 0.77 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 549 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1NX8 · Structure of carbapenem synthase (CarC) complexed with N-acetyl proline · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XB59 · AlphaFold monomer V2.0 prediction for (5R)-carbapenem-3-carboxylate synthase (Q9XB59) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9XB59
- Elsewhere: RCSB PDB 1NX8 · PDBe 1NX8 · UniProt Q9XB59
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.