Research workbench
Crystal structure of ccpc regulatory domain in complex with citrate from bacillus amyloliquefaciens
Analyse Crystal structure of ccpc regulatory domain in complex with citrate from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z72
- Type
- protein
- Length
- 963 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccpc
- UniProt
- A7Z428
- Ligands
- NA
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ccpc | protein | 197 | 37% helix, 28% strand | A7Z428 |
| D | Ccpc | protein | 193 | 38% helix, 27% strand | A7Z428 |
| E | Ccpc | protein | 179 | 30% helix, 31% strand | A7Z428 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E
- FLC · Citrate anion · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.77 | 0.79 | 103 | empty |
| 2 | 64 | 0.67 | 0.95 | 17 | NA, FLC |
| 3 | 66 | 0.66 | 0.94 | 17 | NA, FLC |
| 4 | 69 | 0.66 | 0.93 | 18 | FLC |
| 5 | 64 | 0.66 | 0.94 | 15 | FLC |
Interfaces
6 interfaces between chains.
- A–C · 1280 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1274 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 678 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 192 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Z72 · Crystal structure of CcpC regulatory domain in complex with citrate from Bacillus… · 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 A7Z428
- Elsewhere: RCSB PDB 5Z72 · PDBe 5Z72 · UniProt A7Z428
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