MolNFT v1 · #14162 · protein
Crystal structure of bacteriophage T7 endonuclease I with a wild-type active site
1M0I · Endodeoxyribonuclease I: “Crystal structure of bacteriophage T7 endonuclease I with a wild-type active site”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.63). MolNFT v1 #14162 on GenesisL1: 3D structure…
- PDB
- 1M0I
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endodeoxyribonuclease I
- EC
- 3.1.21.2
- UniProt
- P00641
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endodeoxyribonuclease I (EC 3.1.21.2) | protein | 129 | 31% helix, 25% strand | P00641 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.63 | 0.73 | 55 | SO4 |
| 2 | 74 | 0.44 | 0.81 | 15 | empty |
| 3 | 93 | 0.39 | 0.77 | 22 | empty |
| 4 | 55 | 0.36 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3074 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2746 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1M0I · Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site · the same entry in another collection · chain C against C, 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 P00641
- Elsewhere: RCSB PDB 1M0I · PDBe 1M0I · UniProt P00641
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