MolNFT v1 · #118885 · protein + DNA
Structure of a nuclease-deletion mutant of the type isp restriction- modification enzyme llagi in complex with a DNA substrate mimic
5FFJ · Endonuclease and methylase llagi: “Structure of a nuclease-deletion mutant of the type isp restriction- modification enzyme llagi in complex…”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #118885 on GenesisL1…
- PDB
- 5FFJ
- Type
- protein + DNA
- Length
- 2,365 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease and methylase llagi; DNA (5'- D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*T…
- UniProt
- Q93R01
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease and methylase llagi | protein | 1044 | 43% helix, 15% strand | Q93R01 |
| D | DNA (5'- D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T) -3') | dna | 22 | — | — |
| C, F | DNA (5'- D(P*TP*AP*GP*CP*TP*AP*AP*TP*AP*GP*AP*CP*TP*GP*GP*AP*TP*GP*GP*AP*GP*G) -3') | dna | 22 | — | — |
| B | Endonuclease and methylase llagi | protein | 1232 | 43% helix, 15% strand | Q93R01 |
| E | DNA (5'- D(P*TP*CP*CP*TP*CP*CP*AP*TP*CP*CP*AP*GP*TP*CP*TP*AP*TP*TP*AP*GP*CP*T) -3') | dna | 23 | — | — |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.83 | 0.85 | 95 | empty |
| 2 | 989 | 0.80 | 0.82 | 74 | empty |
| 3 | 205 | 0.79 | 0.94 | 35 | empty |
| 4 | 980 | 0.74 | 0.77 | 88 | empty |
| 5 | 776 | 0.73 | 0.78 | 94 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1569 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–E · 1552 Ų buried · 43 hydrogen bonds · protein-nucleic
- B–F · 1226 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 1179 Ų buried · 21 hydrogen bonds · protein-nucleic
- E–F · 977 Ų buried · 93 hydrogen bonds · nucleic-nucleic
Compared structures
- 5FFJ · Structure of a nuclease-deletion mutant of the Type ISP restriction-modification enzyme… · 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 Q93R01
- Elsewhere: RCSB PDB 5FFJ · PDBe 5FFJ · UniProt Q93R01
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