MolNFT v1 · #38754 · protein + DNA
Structure of rusa D70N in complex with DNA
2H8C · 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3': “Structure of rusa D70N in complex with DNA”. X-ray diffraction, 5 pockets (best druggability 0.68). MolNFT v1 #38754 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2H8C
- Type
- protein + DNA
- Length
- 499 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'; Crossover junction endodeoxyribonuclease rusa
- EC
- 3.1.22.-
- UniProt
- P0AG74
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, W, X | 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3' | dna | 11 | — | — |
| Z | 5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3' | dna | 10 | — | — |
| A | Crossover junction endodeoxyribonuclease rusa (EC 3.1.22.-) | protein | 117 | 30% helix, 33% strand | P0AG74 |
| B | Crossover junction endodeoxyribonuclease rusa (EC 3.1.22.-) | protein | 116 | 32% helix, 33% strand | P0AG74 |
| C | Crossover junction endodeoxyribonuclease rusa (EC 3.1.22.-) | protein | 111 | 32% helix, 31% strand | P0AG74 |
| D | Crossover junction endodeoxyribonuclease rusa (EC 3.1.22.-) | protein | 112 | 33% helix, 29% strand | P0AG74 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.68 | 0.77 | 64 | empty |
| 2 | 325 | 0.52 | 0.74 | 29 | empty |
| 3 | 124 | 0.45 | 0.78 | 23 | empty |
| 4 | 144 | 0.42 | 0.76 | 21 | empty |
| 5 | 51 | 0.34 | 0.79 | 16 | empty |
Interfaces
11 interfaces between chains.
- A–B · 708 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 615 Ų buried · 12 hydrogen bonds · protein-protein
- Y–Z · 464 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- W–X · 456 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- W–B · 314 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
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 P0AG74
- Elsewhere: RCSB PDB 2H8C · PDBe 2H8C · UniProt P0AG74
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