Research workbench
Crystal structure of the restriction-modification controller protein C.CSP231I or operator complex
Analyse Crystal structure of the restriction-modification controller protein C.CSP231I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JCY
- Type
- protein + DNA
- Length
- 226 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CSP231I C protein; DNA (5'- D(*AP*AP*AP*CP*TP*AP*AP*GP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*CP*AP…
- UniProt
- Q32WH4
- Ligands
- IOD
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CSP231I C protein | protein | 92 | 70% helix, 0% strand | Q32WH4 |
| C | DNA (5'- D(*AP*AP*AP*CP*TP*AP*AP*GP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*CP*AP*A)- 3') | dna | 21 | — | — |
| D | DNA (5'- D(*TP*TP*GP*CP*TP*AP*AP*GP*AP*TP*TP*TP*TP*CP*TP*TP*AP*GP*TP*TP*T)- 3') | dna | 21 | — | — |
Ligands and binding sites
- IOD · Iodide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.62 | 0.80 | 33 | empty |
| 2 | 129 | 0.54 | 0.81 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1004 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 939 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- B–D · 392 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 388 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 369 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 4JCY · Crystal structure of the Restriction-Modification Controller Protein C.Csp231I OR… · 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 Q32WH4
- Elsewhere: RCSB PDB 4JCY · PDBe 4JCY · UniProt Q32WH4
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