Research workbench
Crystal structure of C. difficile penicillin-binding protein 2 in complex with ampicillin
Analyse Crystal structure of C. difficile penicillin-binding protein 2 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
- 7RCW
- Type
- protein
- Length
- 822 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein
- UniProt
- C9YK84
- Ligands
- ZZ7, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein | protein | 822 | 40% helix, 17% strand | C9YK84 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.73 | 0.83 | 48 | GOL |
| 2 | 300 | 0.62 | 0.79 | 42 | empty |
| 3 | 327 | 0.55 | 0.75 | 34 | ZZ7 |
| 4 | 60 | 0.45 | 0.83 | 16 | empty |
| 5 | 66 | 0.42 | 0.81 | 21 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RCW · Crystal structure of C. difficile penicillin-binding protein 2 in complex with ampicillin · 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 C9YK84
- Elsewhere: RCSB PDB 7RCW · PDBe 7RCW · UniProt C9YK84
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.