Research workbench
ATP-dependent type isp restriction-modification enzyme llabiii bound to DNA
Analyse ATP-dependent type isp restriction-modification enzyme llabiii bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XQK
- Type
- protein + DNA
- Length
- 3,113 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Llabiii; DNA (28-mer)
- Ligands
- K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Llabiii | protein | 1517 | 42% helix, 17% strand | — |
| B | Llabiii | protein | 1484 | 42% helix, 16% strand | — |
| C, E | DNA (28-mer) | dna | 28 | — | — |
| D, F | DNA (28-mer) | dna | 28 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.85 | 0.87 | 105 | empty |
| 2 | 915 | 0.85 | 0.87 | 98 | empty |
| 3 | 938 | 0.80 | 0.82 | 89 | empty |
| 4 | 798 | 0.79 | 0.83 | 82 | empty |
| 5 | 183 | 0.75 | 0.91 | 20 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1698 Ų buried · 47 hydrogen bonds · protein-nucleic
- B–E · 1667 Ų buried · 50 hydrogen bonds · protein-nucleic
- A–D · 1334 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–F · 1262 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–D · 1239 Ų buried · 123 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XQK · ATP-dependent Type ISP restriction-modification enzyme LlaBIII bound to DNA · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 4XQK · PDBe 4XQK
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