Research workbench
Crystal structure of meganuclease I-smami bound to uncleaveable DNA with a ttct central four
Analyse Crystal structure of meganuclease I-smami bound to uncleaveable DNA with a ttct… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z1Z
- Type
- protein + DNA
- Length
- 697 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meganuclease I-smami; DNA (28-mer)
- UniProt
- F7WD42
- Ligands
- CA
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Meganuclease I-smami | protein | 294 | 47% helix, 19% strand | F7WD42 |
| B | Meganuclease I-smami | protein | 295 | 43% helix, 20% strand | F7WD42 |
| D | DNA (28-mer) | dna | 27 | — | — |
| C | DNA (28-mer) | dna | 27 | — | — |
| F | DNA (28-mer) | dna | 27 | — | — |
| E | DNA (28-mer) | dna | 27 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, D, C, B, F, E
- GOL · Glycerol · additive · 6 copies · chains A, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.71 | 0.80 | 70 | empty |
| 2 | 253 | 0.70 | 0.85 | 42 | empty |
| 3 | 310 | 0.69 | 0.84 | 32 | GOL |
| 4 | 117 | 0.69 | 0.91 | 23 | empty |
| 5 | 304 | 0.65 | 0.82 | 29 | GOL |
Interfaces
9 interfaces between chains.
- A–C · 1395 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–E · 1376 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–C · 1331 Ų buried · 148 hydrogen bonds · nucleic-nucleic
- F–E · 1313 Ų buried · 145 hydrogen bonds · nucleic-nucleic
- A–D · 1274 Ų buried · 24 hydrogen bonds · protein-nucleic
Compared structures
- 4Z1Z · Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTCT 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 4Z1Z · PDBe 4Z1Z · UniProt F7WD42
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