Research workbench
Crystal structure of the mutant D75N I-crei in complex with its wild-type target in presence of ca at the active site (the four central bases, 2NN region, are composed by gtac from 5' to 3')
Analyse Crystal structure of the mutant D75N I-crei in complex with its wild-type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AAG
- 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(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- CA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 54% helix, 20% strand | P05725 |
| E, G | 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP *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, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.75 | 0.95 | 27 | empty |
| 2 | 116 | 0.73 | 0.94 | 29 | empty |
| 3 | 84 | 0.50 | 0.84 | 23 | CA |
| 4 | 62 | 0.41 | 0.82 | 21 | empty |
| 5 | 50 | 0.37 | 0.79 | 11 | empty |
Interfaces
6 interfaces between chains.
- E–G · 1174 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- B–G · 970 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 967 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 935 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–G · 925 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4AAG · Crystal structure of the mutant D75N I-CreI in complex with its wild- type target 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 A against A, TM-score 0.99
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 4AAG · PDBe 4AAG · UniProt P05725
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