Research workbench
Crystal structure of I-crei complexed with its target methylated at position plus 2 (in the B strand) in the presence of calcium
Analyse Crystal structure of I-crei complexed with its target methylated at position… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AQU
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA endonuclease I-crei; 5'-D(*DTP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*DAP…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- CA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 53% helix, 20% strand | P05725 |
| C | 5'-D(*DTP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*DAP *GP*AP*CP*AP*GP*TP*TP*TP*GP*G)-3' | dna | 24 | — | — |
| D | 5'-D(*DCP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CMP *GP*AP*CP*GP*TP*TP*TP*TP*GP*A)-3' | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.73 | 0.96 | 25 | empty |
| 2 | 93 | 0.64 | 0.90 | 27 | empty |
| 3 | 66 | 0.45 | 0.83 | 21 | GOL |
| 4 | 59 | 0.42 | 0.83 | 20 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 1182 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–D · 986 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 980 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 979 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 888 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4AQU · Crystal structure of I-CreI complexed with its target methylated at position plus 2 (in… · the same entry in another collection · chain A against A, TM-score 1.00
- P05725 · AlphaFold monomer V2.0 prediction for DNA endonuclease I-crei (P05725) · a predicted model of the same protein · chain B 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 P05725
- Elsewhere: RCSB PDB 4AQU · PDBe 4AQU · UniProt P05725
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