Research workbench
Crystal structure of a Y37F mutant of the restriction-modification controller protein C.ESP1396I
Analyse Crystal structure of a Y37F mutant of the restriction-modification controller… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I6U
- Type
- protein
- Length
- 461 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Regulatory protein
- UniProt
- Q8GGH0
- Ligands
- NA
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Regulatory protein | protein | 79 | 72% helix, 1% strand | Q8GGH0 |
| B, E, F | Regulatory protein | protein | 77 | 74% helix, 1% strand | Q8GGH0 |
| C | Regulatory protein | protein | 75 | 77% helix, 1% strand | Q8GGH0 |
| D | Regulatory protein | protein | 76 | 74% helix, 1% strand | Q8GGH0 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 3 copies · chains A, D, C, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.56 | 0.88 | 16 | PEG |
| 2 | 207 | 0.49 | 0.76 | 32 | empty |
| 3 | 58 | 0.31 | 0.75 | 11 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1030 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1007 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1001 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 306 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4I6U · Crystal Structure of a Y37F mutant of the Restriction-Modification Controller Protein… · 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 Q8GGH0
- Elsewhere: RCSB PDB 4I6U · PDBe 4I6U · UniProt Q8GGH0
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