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Crystal structure of ccpe regulatory domain in complex with citrate from staphyloccocus aureus
Analyse Crystal structure of ccpe 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
- 5ZZO
- Type
- protein
- Length
- 1,174 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr family transcriptional regulator
- UniProt
- A0A2P8TJ56
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysr family transcriptional regulator | protein | 194 | 37% helix, 32% strand | A0A2P8TJ56 |
| C, D | Lysr family transcriptional regulator | protein | 196 | 36% helix, 32% strand | A0A2P8TJ56 |
| E | Lysr family transcriptional regulator | protein | 195 | 35% helix, 31% strand | A0A2P8TJ56 |
| F | Lysr family transcriptional regulator | protein | 199 | 36% helix, 31% strand | A0A2P8TJ56 |
Ligands and binding sites
- FLC · Citrate anion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.80 | 0.85 | 91 | FLC |
| 2 | 475 | 0.76 | 0.84 | 77 | FLC |
| 3 | 240 | 0.75 | 0.89 | 41 | FLC |
| 4 | 265 | 0.61 | 0.80 | 34 | empty |
| 5 | 315 | 0.59 | 0.77 | 40 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1350 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1307 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1281 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 403 Ų buried · 0 hydrogen bonds · protein-protein
- C–F · 400 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZZO · Crystal structure of CcpE regulatory domain in complex with citrate from Staphyloccocus… · 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 A0A2P8TJ56
- Elsewhere: RCSB PDB 5ZZO · PDBe 5ZZO · UniProt A0A2P8TJ56
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