Research workbench
ECOT38I restriction endonuclease complexed with DNA
Analyse ECOT38I restriction endonuclease complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EDB
- Type
- protein + DNA
- Length
- 722 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ECOT38I restriction endonuclease; DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*TP*CP*AP*CP*G)-3')…
- UniProt
- Q83VS8
- Ligands
- CA, NA, CL
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ECOT38I restriction endonuclease | protein | 350 | 52% helix, 9% strand | Q83VS8 |
| B | ECOT38I restriction endonuclease | protein | 347 | 52% helix, 10% strand | Q83VS8 |
| E | DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*CP*TP*CP*AP*CP*G)-3') | dna | 13 | — | — |
| F | DNA (5'-D(P*CP*GP*TP*GP*AP*GP*CP*TP*CP*TP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, F, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B, E, F
- GOL · Glycerol · additive · 8 copies · chains A, B, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, E, F, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.68 | 0.80 | 36 | PGE |
| 2 | 350 | 0.57 | 0.76 | 46 | empty |
| 3 | 415 | 0.56 | 0.74 | 50 | TRS |
| 4 | 94 | 0.52 | 0.83 | 26 | GOL |
| 5 | 130 | 0.51 | 0.80 | 25 | TRS |
Interfaces
6 interfaces between chains.
- A–B · 1667 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 1138 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–E · 931 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–E · 699 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–F · 586 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7EDB · EcoT38I restriction endonuclease complexed with 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 Q83VS8
- Elsewhere: RCSB PDB 7EDB · PDBe 7EDB · UniProt Q83VS8
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