MolNFT v1 · #30600 · protein + DNA
Structural basis for broad DNA-specificity in integron recombination
2A3V · DNA (31-mer): “Structural basis for broad DNA-specificity in integron recombination”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #30600 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2A3V
- Type
- protein + DNA
- Length
- 1,396 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (31-mer); DNA (34-mer); Site-specific recombinase INTI4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (31-mer) | dna | 31 | — | — |
| F | DNA (34-mer) | dna | 34 | — | — |
| G | DNA (31-mer) | dna | 29 | — | — |
| H | DNA (34-mer) | dna | 32 | — | — |
| A | Site-specific recombinase INTI4 | protein | 313 | 51% helix, 8% strand | — |
| B, D | Site-specific recombinase INTI4 | protein | 320 | 53% helix, 8% strand | — |
| C | Site-specific recombinase INTI4 | protein | 317 | 52% helix, 8% strand | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.86 | 0.88 | 117 | empty |
| 2 | 1127 | 0.86 | 0.87 | 103 | empty |
| 3 | 1053 | 0.81 | 0.83 | 105 | empty |
| 4 | 922 | 0.80 | 0.82 | 102 | empty |
| 5 | 913 | 0.78 | 0.81 | 77 | empty |
Interfaces
20 interfaces between chains.
- B–C · 2138 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 2108 Ų buried · 19 hydrogen bonds · protein-protein
- F–B · 1552 Ų buried · 18 hydrogen bonds · protein-nucleic
- H–D · 1488 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–F · 1376 Ų buried · 124 hydrogen bonds · nucleic-nucleic
Compared structures
- 2A3V · Structural basis for broad DNA-specificity in integron recombination · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 2A3V · PDBe 2A3V
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