Research workbench
Crystal structure of the mariner MOS1 paired end complex with mg
Analyse Crystal structure of the mariner MOS1 paired end complex with mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HOS
- Type
- protein + DNA
- Length
- 832 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposable element mariner, complete cds; MOS1 nts inverted repeat DNA; MOS1 ts…
- EC
- 2.7.7.-
- UniProt
- Q7JQ07
- Ligands
- MG, SO4
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposable element mariner, complete cds (EC 2.7.7.-) | protein | 336 | 47% helix, 13% strand | Q7JQ07 |
| B | Transposable element mariner, complete cds (EC 2.7.7.-) | protein | 337 | 46% helix, 13% strand | Q7JQ07 |
| C, E, G | MOS1 nts inverted repeat DNA | dna | 25 | — | — |
| D, F, H | MOS1 ts inverted repeat DNA | dna | 28 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.76 | 0.83 | 69 | empty |
| 2 | 163 | 0.68 | 0.88 | 26 | empty |
| 3 | 178 | 0.56 | 0.80 | 29 | MG |
| 4 | 244 | 0.54 | 0.77 | 31 | empty |
| 5 | 101 | 0.50 | 0.82 | 20 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2896 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 1136 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- C–D · 1105 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- G–H · 1093 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- B–F · 1059 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3HOS · Crystal structure of the mariner Mos1 paired end complex with Mg · the same entry in another collection · chain H against H, TM-score 1.00
- Q7JQ07 · AlphaFold monomer V2.0 prediction for mariner MOS1 transposase (Q7JQ07) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q7JQ07
- Elsewhere: RCSB PDB 3HOS · PDBe 3HOS · UniProt Q7JQ07
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