MolNFT v1 · #29203 · protein + DNA
Crystal structure of a lambda INTEGRASE(75-356) dimer bound to a coc' core site
1Z19 · 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3': “Crystal structure of a lambda INTEGRASE(75-356) dimer bound to a coc' core site”. X-ray diffraction, 9 pockets (best druggability 0.82). MolNFT v1 #29203 on GenesisL1: 3D…
- PDB
- 1Z19
- Type
- protein + DNA
- Length
- 620 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'…
- UniProt
- P03700
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3' | dna | 12 | — | — |
| D | 5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*T P*TP*A)-3' | dna | 19 | — | — |
| E | 33-mer | dna | 33 | — | — |
| A | Integrase | protein | 273 | 54% helix, 7% strand | P03700 |
| B | Integrase | protein | 283 | 54% helix, 8% strand | P03700 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.82 | 0.89 | 52 | empty |
| 2 | 301 | 0.75 | 0.88 | 39 | empty |
| 3 | 228 | 0.65 | 0.84 | 31 | empty |
| 4 | 413 | 0.62 | 0.77 | 40 | empty |
| 5 | 311 | 0.58 | 0.77 | 30 | empty |
Interfaces
8 interfaces between chains.
- E–A · 1286 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–B · 1112 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 1087 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–A · 1077 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 1054 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered, phosphorylation).
Compared structures
- 1Z19 · Crystal structure of a lambda integrase(75-356) dimer bound to a COC' core site · 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 1Z19 · PDBe 1Z19 · UniProt P03700
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