Research workbench
Crystal structure of the MOS1 mariner paired end complex with mn
Analyse Crystal structure of the MOS1 mariner paired end complex with mn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HOT
- Type
- protein + DNA
- Length
- 835 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
- MN, SO4
- Pockets
- 18 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transposable element mariner, complete cds (EC 2.7.7.-) | protein | 338 | 48% helix, 13% strand | Q7JQ07 |
| B | Transposable element mariner, complete cds (EC 2.7.7.-) | protein | 338 | 48% helix, 14% 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.73 | 0.83 | 55 | MN |
| 2 | 230 | 0.71 | 0.87 | 28 | empty |
| 3 | 364 | 0.71 | 0.83 | 26 | empty |
| 4 | 257 | 0.59 | 0.79 | 25 | empty |
| 5 | 100 | 0.52 | 0.83 | 21 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2988 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1150 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- C–D · 1145 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- G–H · 1135 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- B–F · 1066 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified, 2 disulfide (nucleotide modification, disulfide).
Compared structures
- 3HOT · Crystal structure of the Mos1 mariner paired end complex with Mn · the same entry in another collection · chain G against G, 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 3HOT · PDBe 3HOT · UniProt Q7JQ07
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