Research workbench
Crystal structure of the mutant D75N I-crei in complex with its wild-type target (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
- 4AAB
- 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; 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Ligands
- MG, NA
- Pockets
- 4 · best druggability 0.77
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 |
| D, F | 14MER DNA 5'-D(*TP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*CP)-3' | dna | 14 | — | — |
| E, G | 10MER DNA 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, D, E, F, G
- NA · Sodium ion · metal · chains D, F, G
- PGO · S-1,2-propanediol · additive · 5 copies · chains A, B, D, G, E, F
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 | 108 | 0.77 | 0.97 | 26 | PGO |
| 2 | 110 | 0.71 | 0.93 | 27 | empty |
| 3 | 52 | 0.41 | 0.81 | 14 | empty |
| 4 | 67 | 0.39 | 0.80 | 18 | PGO |
Interfaces
15 interfaces between chains.
- A–B · 976 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 896 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 887 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–G · 791 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–E · 780 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 4AAB · Crystal structure of the mutant D75N I-CreI in complex with its wild- type target (The… · the same entry in another collection · chain G against G, 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 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 4AAB · PDBe 4AAB · UniProt P05725
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