MolNFT v1 · #85375 · protein + DNA
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')
4AAG · DNA endonuclease I-crei: “Crystal structure of the mutant D75N I-crei in complex with its wild-type target in presence of ca at the…”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.75). MolNFT v1 #85375 on…
- 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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