Research workbench
Crystal structure of meganuclease I-smami bound to uncleaveable DNA with a ttgt central four
Analyse Crystal structure of meganuclease I-smami bound to uncleaveable DNA with a ttgt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z20
- Type
- protein + DNA
- Length
- 693 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meganuclease I-smami; DNA (26-mer)
- UniProt
- F7WD42
- Ligands
- CA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meganuclease I-smami | protein | 298 | 47% helix, 20% strand | F7WD42 |
| C, F | DNA (26-mer) | dna | 26 | — | — |
| B, E | DNA (26-mer) | dna | 26 | — | — |
| D | Meganuclease I-smami | protein | 291 | 49% helix, 21% strand | F7WD42 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, C, B, D, F, E
- GOL · Glycerol · additive · 3 copies · chains C, B, A, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.75 | 0.81 | 73 | empty |
| 2 | 684 | 0.74 | 0.81 | 69 | CA |
| 3 | 145 | 0.71 | 0.91 | 38 | empty |
| 4 | 55 | 0.70 | 0.98 | 27 | empty |
| 5 | 50 | 0.69 | 0.98 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1391 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 1379 Ų buried · 29 hydrogen bonds · protein-nucleic
- D–F · 1326 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–C · 1247 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–B · 1242 Ų buried · 135 hydrogen bonds · nucleic-nucleic
Compared structures
- 4Z20 · Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTGT Central… · 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 F7WD42
- Elsewhere: RCSB PDB 4Z20 · PDBe 4Z20 · UniProt F7WD42
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