MolNFT v1 · #126392 · protein
Crystal structure of the large terminase nuclease from thermophilic phage G20C with bound cobalt
5M1O · Phage terminase large subunit: “Crystal structure of the large terminase nuclease from thermophilic phage G20C with bound cobalt”. X-ray diffraction, 1 ligand (CO), 1 pocket (best druggability 0.80). MolNFT v1 #126392 on GenesisL1…
- PDB
- 5M1O
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage terminase large subunit
- Ligands
- CO
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phage terminase large subunit | protein | 188 | 32% helix, 28% strand | — |
| B | Phage terminase large subunit | protein | 188 | 31% helix, 27% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.80 | 0.86 | 65 | CO |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5M1O · Crystal structure of the large terminase nuclease from thermophilic phage G20c with bound… · 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
- Elsewhere: RCSB PDB 5M1O · PDBe 5M1O
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