Research workbench
Y33H mutant of homing endonuclease I-crei
Analyse Y33H mutant of homing endonuclease I-crei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U0D
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3'…
- EC
- 3.1.-.-
- UniProt
- P05725
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP *GP*TP*TP*CP*CP*G)-3' | dna | 24 | — | — |
| D | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP *TP*TP*TP*CP*GP*C)-3' | dna | 24 | — | — |
| A, B | DNA endonuclease I-crei (EC 3.1.-.-) | protein | 152 | 49% helix, 20% strand | P05725 |
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.75 | 0.96 | 27 | empty |
| 2 | 130 | 0.68 | 0.90 | 29 | empty |
| 3 | 90 | 0.54 | 0.86 | 25 | empty |
| 4 | 81 | 0.52 | 0.85 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1165 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- C–A · 985 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 985 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 977 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–A · 822 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
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 1U0D · PDBe 1U0D · UniProt P05725
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