MolNFT v1 · #16379 · protein
The crystal structure of carbapenem synthase (carc)
1NX4: “The crystal structure of carbapenem synthase (carc)”. X-ray diffraction, 2 ligands (AKG, FE), 12 pockets (best druggability 0.68). MolNFT v1 #16379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NX4
- Type
- protein
- Length
- 753 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem synthase
- UniProt
- Q9XB59
- Ligands
- AKG, FE
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem synthase | protein | 247 | 23% helix, 30% strand | Q9XB59 |
| B | Carbapenem synthase | protein | 256 | 22% helix, 29% strand | Q9XB59 |
| C | Carbapenem synthase | protein | 250 | 24% helix, 30% strand | Q9XB59 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.68 | 0.83 | 37 | AKG |
| 2 | 171 | 0.63 | 0.84 | 29 | FE, AKG |
| 3 | 215 | 0.61 | 0.81 | 37 | FE, AKG |
| 4 | 229 | 0.56 | 0.78 | 37 | empty |
| 5 | 295 | 0.55 | 0.76 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 545 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 534 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 1NX4 · The crystal structure of carbapenem synthase (CarC) · 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 A 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 1NX4 · PDBe 1NX4 · UniProt Q9XB59
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.