MolNFT v1 · #62295 · protein + DNA
Structure of N141A hincii with cognate DNA
3EBC · Type-2 restriction enzyme hincii: “Structure of N141A hincii with cognate DNA”. X-ray diffraction, 1 ligand (MN), 8 pockets (best druggability 0.71). MolNFT v1 #62295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EBC
- Type
- protein + DNA
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme hincii; 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DG…
- EC
- 3.1.21.4
- UniProt
- P17743
- Ligands
- MN
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type-2 restriction enzyme hincii (EC 3.1.21.4) | protein | 241 | 48% helix, 22% strand | P17743 |
| B | Type-2 restriction enzyme hincii (EC 3.1.21.4) | protein | 244 | 43% helix, 22% strand | P17743 |
| E | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*D C)-3' | dna | 14 | — | — |
| F | 5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*D C)-3' | dna | 14 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.71 | 0.81 | 59 | MN |
| 2 | 348 | 0.67 | 0.82 | 28 | empty |
| 3 | 284 | 0.66 | 0.82 | 35 | empty |
| 4 | 318 | 0.65 | 0.81 | 25 | empty |
| 5 | 114 | 0.50 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1278 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 687 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–F · 666 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–E · 653 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–E · 591 Ų buried · 12 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 P17743
- Elsewhere: RCSB PDB 3EBC · PDBe 3EBC · UniProt P17743
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