Research workbench
Deinococcus radiodurans ISDRA2 transposase left end DNA complex
Analyse Deinococcus radiodurans ISDRA2 transposase left end DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XM3
- Type
- protein + DNA
- Length
- 956 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transposase; DRA2 transposase binding element; 5'-D(*TP*TP*AP*GP*T)-3'
- UniProt
- O83028
- Ligands
- MG
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Transposase | protein | 126 | 40% helix, 32% strand | O83028 |
| B | Transposase | protein | 129 | 40% helix, 29% strand | O83028 |
| C | Transposase | protein | 128 | 40% helix, 30% strand | O83028 |
| D | Transposase | protein | 129 | 42% helix, 29% strand | O83028 |
| G, I, K, M, O, Q | DRA2 transposase binding element | dna | 27 | — | — |
| H, J, L, N, P, R | 5'-D(*TP*TP*AP*GP*T)-3' | dna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains E, F, O, Q, A, B, G, I, C, D, K, M
- GOL · Glycerol · additive · 4 copies · chains A, G, H, B, I, J, C, D, K, L, E, F, O, P
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.62 | 0.80 | 31 | MG |
| 2 | 177 | 0.59 | 0.82 | 22 | MG |
| 3 | 208 | 0.58 | 0.81 | 24 | MG |
| 4 | 193 | 0.58 | 0.81 | 22 | MG |
| 5 | 209 | 0.57 | 0.80 | 23 | MG |
Interfaces
35 interfaces between chains.
- C–D · 1558 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1377 Ų buried · 23 hydrogen bonds · protein-protein
- C–K · 909 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–G · 909 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 2XM3 · Deinococcus radiodurans ISDra2 Transposase Left end DNA complex · 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 O83028
- Elsewhere: RCSB PDB 2XM3 · PDBe 2XM3 · UniProt O83028
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