Research workbench
Crystal structure of the lambda integrase (residues 75-356) bound to DNA
Analyse Crystal structure of the lambda integrase (residues 75-356) bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P7D
- Type
- protein + DNA
- Length
- 638 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'; 26-mer; Integrase
- UniProt
- P03700
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3' | dna | 13 | — | — |
| D, F | 26-mer | dna | 26 | — | — |
| A, B | Integrase | protein | 280 | 51% helix, 8% strand | P03700 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.69 | 0.87 | 30 | empty |
| 2 | 452 | 0.67 | 0.79 | 42 | empty |
| 3 | 348 | 0.66 | 0.81 | 45 | empty |
| 4 | 92 | 0.66 | 0.91 | 22 | empty |
| 5 | 323 | 0.56 | 0.76 | 31 | empty |
Interfaces
7 interfaces between chains.
- D–A · 1409 Ų buried · 30 hydrogen bonds · protein-nucleic
- F–B · 1349 Ų buried · 33 hydrogen bonds · protein-nucleic
- C–A · 975 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–B · 964 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 658 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1P7D · Crystal structure of the Lambda Integrase (residues 75-356) bound to DNA · the same entry in another collection · chain C against C, 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 P03700
- Elsewhere: RCSB PDB 1P7D · PDBe 1P7D · UniProt P03700
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