Research workbench
The homing endonuclease I-scei bound to its DNA recognition region
Analyse The homing endonuclease I-scei bound to its DNA recognition region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R7M
- Type
- protein + DNA
- Length
- 542 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP *TP*AP*AP*TP*AP*C)-3'…
- EC
- 3.1.-.-
- UniProt
- P03882
- Ligands
- CA
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'- D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP*CP*AP*GP*GP*GP *TP*AP*AP*TP*AP*C)-3' | dna | 24 | — | — |
| D, F | 5'- D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP*AP*TP*CP*CP*CP *TP*AP*GP*CP*GP*T)-3' | dna | 24 | — | — |
| A, B | Intron-encoded endonuclease I-scei (EC 3.1.-.-) | protein | 223 | 43% helix, 21% strand | P03882 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains C, D, E, F, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.68 | 0.78 | 70 | CA |
| 2 | 70 | 0.59 | 0.90 | 24 | empty |
| 3 | 65 | 0.59 | 0.90 | 25 | empty |
| 4 | 265 | 0.59 | 0.79 | 29 | empty |
| 5 | 217 | 0.55 | 0.79 | 40 | CA |
Interfaces
9 interfaces between chains.
- C–A · 1304 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–A · 1258 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–B · 1250 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–B · 1247 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–D · 1152 Ų buried · 82 hydrogen bonds · nucleic-nucleic
Compared structures
- 1R7M · The homing endonuclease I-SceI bound to its DNA recognition region · the same entry in another collection · chain E against E, TM-score 1.00
- P03882 · AlphaFold monomer V2.0 prediction for intron-encoded endonuclease I-scei (P03882) · 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 P03882
- Elsewhere: RCSB PDB 1R7M · PDBe 1R7M · UniProt P03882
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