MolNFT v1 · #102354 · protein
Crystal structure of carbapenem synthase in complex with (3S,5S)- carbapenam
4OJ8 · (5R)-carbapenem-3-carboxylate synthase: “Crystal structure of carbapenem synthase in complex with (3S,5S)- carbapenam”. X-ray diffraction, 3 ligands (AKG, 2TQ, FE2), 9 pockets (best druggability 0.83). MolNFT v1 #102354 on…
- PDB
- 4OJ8
- Type
- protein
- Length
- 795 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (5R)-carbapenem-3-carboxylate synthase
- EC
- 1.14.20.3
- UniProt
- Q9XB59
- Ligands
- AKG, 2TQ, FE2
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (5R)-carbapenem-3-carboxylate synthase (EC 1.14.20.3) | protein | 253 | 24% helix, 30% strand | Q9XB59 |
| B, C | (5R)-carbapenem-3-carboxylate synthase (EC 1.14.20.3) | protein | 271 | 26% helix, 28% strand | Q9XB59 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- 2TQ · (2S,5S)-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · 2 copies · chains B, C
- FE2 · Fe (II) ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.83 | 0.84 | 106 | GOL |
| 2 | 120 | 0.80 | 0.98 | 28 | FE2, AKG, 2TQ |
| 3 | 118 | 0.80 | 0.98 | 28 | FE2, AKG, 2TQ |
| 4 | 220 | 0.60 | 0.80 | 34 | FE2, AKG |
| 5 | 69 | 0.34 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 64 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OJ8 · Crystal structure of carbapenem synthase in complex with (3S,5S)-carbapenam · 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 0.97
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 4OJ8 · PDBe 4OJ8 · UniProt Q9XB59
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