Research workbench
Structural basis underlying complex assembly andconformational transition of the type I R-M system
Analyse Structural basis underlying complex assembly andconformational transition of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YBB
- Type
- protein + DNA
- Length
- 1,858 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction-modification system methyltransferase subunit; Restriction…
- UniProt
- Q8R9Q4, Q8R9Q6
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type I restriction-modification system methyltransferase subunit | protein | 487 | 49% helix, 11% strand | Q8R9Q4 |
| C, E | Type I restriction-modification system methyltransferase subunit | protein | 30 | 87% helix, 0% strand | Q8R9Q4 |
| D, G | Restriction endonuclease S subunits | protein | 390 | 38% helix, 21% strand | Q8R9Q6 |
| H | DNA | dna | 22 | — | — |
| I | DNA | dna | 22 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.80 | 0.82 | 114 | empty |
| 2 | 1084 | 0.76 | 0.79 | 116 | empty |
| 3 | 1017 | 0.75 | 0.78 | 68 | empty |
| 4 | 562 | 0.73 | 0.81 | 76 | empty |
| 5 | 949 | 0.73 | 0.77 | 62 | empty |
Interfaces
12 interfaces between chains.
- B–G · 1798 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1769 Ų buried · 5 hydrogen bonds · protein-protein
- H–I · 997 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- E–G · 856 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YBB · Structural basis underlying complex assembly andconformational transition of the type I… · the same entry in another collection · chain D against D, 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 Q8R9Q4
- Every structure of UniProt Q8R9Q6
- Elsewhere: RCSB PDB 5YBB · PDBe 5YBB · UniProt Q8R9Q4 · UniProt Q8R9Q6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.