MolNFT v1 · #14928 · protein + DNA
E-DREI
1MOW · 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP…: “E-DREI”. X-ray diffraction, 2 ligands (MG, SO4), 17 pockets (best druggability 0.85). MolNFT v1 #14928 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1MOW
- Type
- protein + DNA
- Length
- 1,147 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP *CP*GP*GP*CP*G)-3'…
- EC
- 3.1.-.-
- UniProt
- P21505, P05725
- Ligands
- MG, SO4
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E, H, K | 5'-D(*CP*CP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*AP*GP*TP*TP*CP *CP*GP*GP*CP*G)-3' | dna | 23 | — | — |
| C, F, I, L | 5'-D(*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*GP*AP*GP*AP*CP*AP*GP *TP*TP*TP*GP*G)-3' | dna | 23 | — | — |
| A, D | Chimera of homing endonuclease I-dmoi and DNA endonuclease I-crei (EC 3.1.-.-) | protein | 248 | 54% helix, 25% strand | P21505, P05725 |
| G | Chimera of homing endonuclease I-dmoi and DNA endonuclease I-crei (EC 3.1.-.-) | protein | 233 | 48% helix, 22% strand | P21505, P05725 |
| J | Chimera of homing endonuclease I-dmoi and DNA endonuclease I-crei (EC 3.1.-.-) | protein | 234 | 49% helix, 21% strand | P21505, P05725 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains E, F, D, B, C, A
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, D
- GOL · Glycerol · additive · 18 copies · chains B, C, F, D, E, A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.85 | 0.86 | 106 | empty |
| 2 | 780 | 0.84 | 0.88 | 92 | empty |
| 3 | 676 | 0.74 | 0.81 | 87 | empty |
| 4 | 320 | 0.74 | 0.86 | 47 | empty |
| 5 | 279 | 0.71 | 0.86 | 45 | empty |
Interfaces
26 interfaces between chains.
- F–D · 1669 Ų buried · 45 hydrogen bonds · protein-nucleic
- C–A · 1648 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–A · 1570 Ų buried · 35 hydrogen bonds · protein-nucleic
- E–D · 1566 Ų buried · 35 hydrogen bonds · protein-nucleic
- E–F · 1163 Ų buried · 98 hydrogen bonds · nucleic-nucleic
Compared structures
- 1MOW · E-DreI · the same entry in another collection · chain J against J, 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 P21505
- Every structure of UniProt P05725
- Elsewhere: RCSB PDB 1MOW · PDBe 1MOW · UniProt P21505 · UniProt P05725
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