MolNFT v1 · #186410 · protein
Crystal structure of C. difficile penicillin-binding protein 2 in complex with ceftobiprole
7RCY: “Crystal structure of C. difficile penicillin-binding protein 2 in complex with ceftobiprole”. X-ray diffraction, 2 ligands (RB6, ZN), 9 pockets (best druggability 0.82). MolNFT v1 #186410 on GenesisL1: 3D structure, binding sites…
- PDB
- 7RCY
- Type
- protein
- Length
- 828 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein
- UniProt
- C9YK84
- Ligands
- RB6, ZN
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein | protein | 828 | 41% helix, 15% strand | C9YK84 |
Ligands and binding sites
- RB6 · (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
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 | 1128 | 0.82 | 0.83 | 83 | empty |
| 2 | 506 | 0.73 | 0.82 | 45 | empty |
| 3 | 532 | 0.69 | 0.79 | 57 | RB6 |
| 4 | 236 | 0.53 | 0.77 | 37 | empty |
| 5 | 108 | 0.43 | 0.78 | 20 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7RCY · Crystal structure of C. difficile penicillin-binding protein 2 in complex with… · 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 7RCY · PDBe 7RCY · UniProt C9YK84
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