MolNFT v1 · #70433 · protein
Crystal structure of the type I restriction-modification system methyltransferase subunit from streptococcus thermophilus, northeast structural genomics consortium target SUR80
3LKD: “Crystal structure of the type I restriction-modification system methyltransferase subunit from streptococcus…”. X-ray diffraction, 13 pockets (best druggability 0.69). MolNFT v1 #70433 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3LKD
- Type
- protein
- Length
- 940 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction-modification system methyltransferase subunit
- UniProt
- Q5M500
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction-modification system methyltransferase subunit | protein | 468 | 46% helix, 12% strand | Q5M500 |
| B | Type I restriction-modification system methyltransferase subunit | protein | 472 | 47% helix, 12% strand | Q5M500 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.69 | 0.83 | 51 | empty |
| 2 | 348 | 0.68 | 0.82 | 56 | empty |
| 3 | 285 | 0.62 | 0.80 | 31 | empty |
| 4 | 273 | 0.59 | 0.79 | 32 | empty |
| 5 | 223 | 0.49 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3LKD · Crystal Structure of the type I restriction-modification system methyltransferase subunit… · 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 Q5M500
- Elsewhere: RCSB PDB 3LKD · PDBe 3LKD · UniProt Q5M500
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