Research workbench
Crystal structure of C. difficile spovd in complex with ampicillin
Analyse Crystal structure of C. difficile spovd in complex with ampicillin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RCZ
- Type
- protein
- Length
- 1,014 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Stage V sporulation protein D (sporulation specific penicillin-binding protein)
- UniProt
- C9YPN0
- Ligands
- ZZ7, ZN, SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Stage V sporulation protein D (sporulation specific penicillin-binding protein) | protein | 511 | 37% helix, 25% strand | C9YPN0 |
| B | Stage V sporulation protein D (sporulation specific penicillin-binding protein) | protein | 503 | 37% helix, 24% strand | C9YPN0 |
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 · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
- POL · N-propanol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.76 | 0.81 | 83 | SO4, ZZ7 |
| 2 | 607 | 0.67 | 0.77 | 56 | PEG |
| 3 | 284 | 0.52 | 0.74 | 30 | ZZ7 |
| 4 | 127 | 0.52 | 0.81 | 23 | SO4 |
| 5 | 109 | 0.51 | 0.81 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 933 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RCZ · Crystal structure of C. difficile SpoVD 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 C9YPN0
- Elsewhere: RCSB PDB 7RCZ · PDBe 7RCZ · UniProt C9YPN0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.