MolNFT v1 · #20518 · protein + DNA
Bacteriophage lambda excisionase (xis)-DNA complex
1RH6 · 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3': “Bacteriophage lambda excisionase (xis)-DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #20518 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1RH6
- Type
- protein + DNA
- Length
- 135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3'…
- UniProt
- P03699
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3' | dna | 14 | — | — |
| D | 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3' | dna | 14 | — | — |
| A | Excisionase | protein | 55 | 27% helix, 25% strand | P03699 |
| B | Excisionase | protein | 52 | 31% helix, 29% strand | P03699 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 379 | 0.68 | 0.82 | 25 | empty |
| 2 | 178 | 0.44 | 0.75 | 24 | empty |
| 3 | 52 | 0.23 | 0.72 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 620 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- D–B · 464 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 446 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 237 Ų buried · 3 hydrogen bonds · protein-protein
- D–A · 135 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 1RH6 · Bacteriophage Lambda Excisionase (Xis)-DNA Complex · 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 P03699
- Elsewhere: RCSB PDB 1RH6 · PDBe 1RH6 · UniProt P03699
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