MolNFT v1 · #117038 · protein + DNA
Crystal structure of specific restriction endonuclease agei-DNA complex
5DWB · Type-2 restriction enzyme agei: “Crystal structure of specific restriction endonuclease agei-DNA complex”. X-ray diffraction, 5 pockets (best druggability 0.64). MolNFT v1 #117038 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DWB
- Type
- protein + DNA
- Length
- 582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type-2 restriction enzyme agei; DNA (5'-D(*TP*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*GP*A*)-3')
- EC
- 3.1.21.4
- UniProt
- Q9KHV6
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type-2 restriction enzyme agei (EC 3.1.21.4) | protein | 278 | 40% helix, 16% strand | Q9KHV6 |
| C, D | DNA (5'-D(*TP*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*GP*A*)-3') | dna | 13 | — | — |
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.64 | 0.83 | 31 | empty |
| 2 | 490 | 0.64 | 0.77 | 57 | empty |
| 3 | 208 | 0.61 | 0.82 | 31 | empty |
| 4 | 207 | 0.51 | 0.77 | 33 | empty |
| 5 | 190 | 0.50 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–C · 862 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–C · 852 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 849 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 842 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–D · 680 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Compared structures
- 5DWB · Crystal structure of specific restriction endonuclease AgeI-DNA complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KHV6 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme agei (Q9KHV6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9KHV6
- Elsewhere: RCSB PDB 5DWB · PDBe 5DWB · UniProt Q9KHV6
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