Research workbench
Crystal structure of a lambda integrase dimer bound to a coc' core site
Analyse Crystal structure of a lambda integrase dimer bound to a coc' core site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z1B
- Type
- protein + DNA
- Length
- 807 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'…
- UniProt
- P03700
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*T*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3' | dna | 11 | — | — |
| D | 5'-D(*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T) -3' | dna | 18 | — | — |
| E | 29-mer DNA | dna | 29 | — | — |
| F | 26-mer DNA | dna | 25 | — | — |
| G | 26-mer DNA | dna | 25 | — | — |
| A | Integrase | protein | 349 | 51% helix, 11% strand | P03700 |
| B | Integrase | protein | 350 | 51% helix, 9% strand | P03700 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.68 | 0.79 | 45 | empty |
| 2 | 477 | 0.67 | 0.79 | 47 | empty |
| 3 | 386 | 0.60 | 0.77 | 34 | empty |
| 4 | 255 | 0.46 | 0.73 | 23 | empty |
| 5 | 182 | 0.45 | 0.75 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1268 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1075 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–B · 1028 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–B · 1006 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–E · 639 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1Z1B · Crystal structure of a lambda integrase dimer bound to a COC' core site · the same entry in another collection · chain D against D, 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 1Z1B · PDBe 1Z1B · UniProt P03700
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