Research workbench
Crystal structure of a lambda integrase tetramer bound to a holliday junction
Analyse Crystal structure of a lambda integrase tetramer bound to a holliday junction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z1G
- Type
- protein + DNA
- Length
- 1,584 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 29-mer; 5'-D(*AP*CP*AP*GP*GP*TP*CP*AP*CP*TP*AP*TP*CP*AP*GP*TP*CP*AP…
- UniProt
- P03700
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | 29-mer | dna | 29 | — | — |
| J | 29-mer | dna | 29 | — | — |
| K | 29-mer | dna | 29 | — | — |
| L | 29-mer | dna | 29 | — | — |
| E, G | 5'-D(*AP*CP*AP*GP*GP*TP*CP*AP*CP*TP*AP*TP*CP*AP*GP*TP*CP*AP *AP*AP*AP*TP*AP*CP*C)-3' | dna | 24 | — | — |
| F, H | 25-mer | dna | 25 | — | — |
| A, C | Integrase | protein | 349 | 48% helix, 9% strand | P03700 |
| B, D | Integrase | protein | 336 | 49% helix, 9% strand | P03700 |
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 | 928 | 0.81 | 0.84 | 71 | empty |
| 2 | 1139 | 0.81 | 0.83 | 93 | empty |
| 3 | 721 | 0.69 | 0.77 | 61 | empty |
| 4 | 496 | 0.65 | 0.78 | 57 | empty |
| 5 | 54 | 0.64 | 0.94 | 17 | empty |
Interfaces
31 interfaces between chains.
- C–D · 1472 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1451 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1354 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1266 Ų buried · 2 hydrogen bonds · protein-protein
- J–B · 1188 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 1Z1G · Crystal structure of a lambda integrase tetramer bound to a Holliday junction · the same entry in another collection · chain I against I, 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 1Z1G · PDBe 1Z1G · UniProt P03700
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