Research workbench
Crystal structure of mMsoI/DNA complex with calcium
Analyse Crystal structure of mMsoI/DNA complex with calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FD2
- Type
- protein + DNA
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.69
- Source
- Monomastix sp. (strain OKE-1); Monomastix sp. OKE-1, unidentified; SYNTHETIC…
- Molecule
- Site-specific DNA endonuclease I-MsoI; 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*…
- EC
- 3.1.-.-
- UniProt
- C0JWR6
- Ligands
- CA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.69 · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Site-specific DNA endonuclease I-MsoI (EC 3.1.-.-) | protein | 338 | 48% helix, 18% strand | C0JWR6 |
| B | 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | dna | 24 | — | — |
| C | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3' | dna | 24 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.61 | 0.79 | 41 | CA |
| 2 | 293 | 0.59 | 0.79 | 32 | empty |
| 3 | 73 | 0.35 | 0.77 | 16 | empty |
| 4 | 59 | 0.32 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1552 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 1513 Ų buried · 35 hydrogen bonds · protein-nucleic
- B–C · 1206 Ų buried · 115 hydrogen bonds · nucleic-nucleic
Compared structures
- 3FD2 · Crystal structure of MMSOI/DNA complex with calcium · 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 C0JWR6
- Elsewhere: RCSB PDB 3FD2 · PDBe 3FD2 · UniProt C0JWR6
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