MolNFT v1 · #176441 · protein
Crystal structure of ccpc regulatory domain in complex with citrate from bacillus amyloliquefaciens
7DMW: “Crystal structure of ccpc regulatory domain in complex with citrate from bacillus amyloliquefaciens”. X-ray diffraction, 13 pockets (best druggability 0.77). MolNFT v1 #176441 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DMW
- Type
- protein
- Length
- 976 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccpc
- UniProt
- A7Z428
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ccpc | protein | 200 | 37% helix, 29% strand | A7Z428 |
| B | Ccpc | protein | 199 | 38% helix, 30% strand | A7Z428 |
| D | Ccpc | protein | 195 | 37% helix, 29% strand | A7Z428 |
| E | Ccpc | protein | 182 | 36% helix, 30% strand | A7Z428 |
Ligands and binding sites
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.77 | 0.81 | 82 | empty |
| 2 | 54 | 0.67 | 0.96 | 15 | FLC |
| 3 | 54 | 0.66 | 0.95 | 16 | FLC |
| 4 | 59 | 0.66 | 0.95 | 17 | FLC |
| 5 | 50 | 0.65 | 0.95 | 15 | FLC |
Interfaces
6 interfaces between chains.
- A–C · 1265 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1223 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 668 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 193 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7DMW · 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 7DMW · PDBe 7DMW · UniProt A7Z428
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