Research workbench
Crystal structure of laglidadg meganuclease I-cpami bound to uncleaved DNA
Analyse Crystal structure of laglidadg meganuclease I-cpami bound to uncleaved DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIS
- Type
- protein + DNA
- Length
- 691 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meganuclease I-cpami; DNA (28-mer)
- UniProt
- O20960
- Ligands
- CA
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meganuclease I-cpami | protein | 295 | 51% helix, 20% strand | O20960 |
| B | Meganuclease I-cpami | protein | 284 | 52% helix, 20% strand | O20960 |
| E, C | DNA (28-mer) | dna | 28 | — | — |
| F, D | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, F, E, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, E, F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.66 | 0.83 | 32 | empty |
| 2 | 320 | 0.66 | 0.82 | 33 | empty |
| 3 | 383 | 0.62 | 0.78 | 42 | EDO |
| 4 | 211 | 0.48 | 0.75 | 26 | empty |
| 5 | 168 | 0.47 | 0.76 | 24 | EDO |
Interfaces
8 interfaces between chains.
- A–F · 1513 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–C · 1455 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–E · 1444 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–D · 1352 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- E–F · 1349 Ų buried · 109 hydrogen bonds · nucleic-nucleic
Compared structures
- 4YIS · Crystal Structure of LAGLIDADG Meganuclease I-CpaMI Bound to Uncleaved DNA · the same entry in another collection · 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 O20960
- Elsewhere: RCSB PDB 4YIS · PDBe 4YIS · UniProt O20960
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