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Restriction endonuclease in complex with substrate DNA
Analyse Restriction endonuclease in complex with substrate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NDH
- Type
- protein + DNA
- Length
- 442 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Restriction endonuclease thai; DNA (5'-D(*G*GP*TP*AP*CP*GP*CP*GP*AP*TP*G)-3'); DNA…
- UniProt
- Q9HJY3
- Ligands
- NA, CL, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Restriction endonuclease thai | protein | 214 | 42% helix, 21% strand | Q9HJY3 |
| B | Restriction endonuclease thai | protein | 208 | 41% helix, 22% strand | Q9HJY3 |
| C | DNA (5'-D(*G*GP*TP*AP*CP*GP*CP*GP*AP*TP*G)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*C*CP*AP*TP*CP*GP*CP*GP*TP*AP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.69 | 0.84 | 50 | PGE |
| 2 | 128 | 0.49 | 0.80 | 26 | empty |
| 3 | 115 | 0.47 | 0.80 | 25 | empty |
| 4 | 115 | 0.46 | 0.79 | 29 | empty |
| 5 | 111 | 0.40 | 0.76 | 16 | SO4 |
Interfaces
6 interfaces between chains.
- A–B · 2734 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 952 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 948 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–D · 470 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- A–D · 384 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3NDH · Restriction endonuclease in complex with substrate DNA · the same entry in another collection · chain A against A, 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 Q9HJY3
- Elsewhere: RCSB PDB 3NDH · PDBe 3NDH · UniProt Q9HJY3
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