MolNFT v1 · #141439 · protein
Crystal structure of ccpe regulatory domain in citrate-bound form from staphyloccocus aureus
5Z7H · Lysr family transcriptional regulator: “Crystal structure of ccpe regulatory domain in citrate-bound form from staphyloccocus aureus”. X-ray diffraction, 6 pockets (best druggability 0.73). MolNFT v1 #141439 on GenesisL1: 3D…
- PDB
- 5Z7H
- Type
- protein
- Length
- 1,167 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr family transcriptional regulator
- UniProt
- A0A0D1IHL7
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysr family transcriptional regulator | protein | 193 | 36% helix, 31% strand | A0A0D1IHL7 |
| B | Lysr family transcriptional regulator | protein | 196 | 36% helix, 31% strand | A0A0D1IHL7 |
| D | Lysr family transcriptional regulator | protein | 197 | 36% helix, 32% strand | A0A0D1IHL7 |
| E, F | Lysr family transcriptional regulator | protein | 194 | 38% helix, 30% strand | A0A0D1IHL7 |
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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.73 | 0.88 | 46 | FLC |
| 2 | 310 | 0.73 | 0.86 | 51 | FLC |
| 3 | 255 | 0.70 | 0.86 | 49 | FLC |
| 4 | 301 | 0.60 | 0.78 | 35 | empty |
| 5 | 323 | 0.58 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- E–F · 1333 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1320 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1300 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5Z7H · Crystal structure of CcpE regulatory domain in citrate-bound form from Staphyloccocus… · the same entry in another collection · chain B against B, 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 A0A0D1IHL7
- Elsewhere: RCSB PDB 5Z7H · PDBe 5Z7H · UniProt A0A0D1IHL7
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