Research workbench
Structure of bacteriophage T4 endoii E118A mutant
Analyse Structure of bacteriophage T4 endoii E118A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WSH
- Type
- protein
- Length
- 527 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease II
- EC
- 3.1.21.-
- UniProt
- P07059
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease II (EC 3.1.21.-) | protein | 134 | 32% helix, 32% strand | P07059 |
| B | Endonuclease II (EC 3.1.21.-) | protein | 131 | 34% helix, 32% strand | P07059 |
| C | Endonuclease II (EC 3.1.21.-) | protein | 129 | 34% helix, 33% strand | P07059 |
| D | Endonuclease II (EC 3.1.21.-) | protein | 133 | 33% helix, 33% strand | P07059 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 178 | 0.71 | 0.88 | 26 | empty |
| 2 | 94 | 0.70 | 0.94 | 22 | empty |
| 3 | 91 | 0.36 | 0.75 | 14 | empty |
| 4 | 50 | 0.29 | 0.76 | 17 | empty |
| 5 | 55 | 0.24 | 0.71 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 688 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 394 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2WSH · Structure of bacteriophage T4 EndoII E118A mutant · 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 P07059
- Elsewhere: RCSB PDB 2WSH · PDBe 2WSH · UniProt P07059
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