MolNFT v1 · #85917 · protein + DNA
Crystal structure of I-crei complexed with its target methylated at position plus 2 (in the B strand) in the presence of magnesium
4AQX · DNA endonuclease I-crei: “Crystal structure of I-crei complexed with its target methylated at position plus 2 (in the B strand) in the…”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.70). MolNFT v1 #85917 on…
- PDB
- 4AQX
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 6
- 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*GP*AP)-3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 55% helix, 21% strand | P05725 |
| C | 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP)-3' | dna | 14 | — | — |
| D | 5'-D(*GP*AP*CP*AP*GP*TP*TP*TP*GP*GP)-3' | dna | 10 | — | — |
| E | 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*5CM)-3' | dna | 14 | — | — |
| F | 5'-D(*GP*AP*CP*GP*TP*TP*TP*TP*GP*AP)-3' | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, B, D, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.70 | 0.96 | 23 | empty |
| 2 | 76 | 0.64 | 0.92 | 25 | GOL |
| 3 | 55 | 0.36 | 0.80 | 16 | empty |
Interfaces
15 interfaces between chains.
- A–B · 931 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 881 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 874 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 811 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 803 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4AQX · Crystal structure of I-CreI complexed with its target methylated at position plus 2 (in… · the same entry in another collection · chain E against E, 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 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 4AQX · PDBe 4AQX · UniProt P05725
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