Research workbench
Crystal structure of pdf from the vibrio parahaemolyticus bacteriophage VP16T - crystal form II
Analyse Crystal structure of pdf from the vibrio parahaemolyticus bacteriophage VP16T… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MTD
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein ORF60T
- UniProt
- Q6VT21
- Ligands
- NI, ZN
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein ORF60T | protein | 137 | 25% helix, 35% strand | Q6VT21 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.64 | 0.79 | 42 | empty |
| 2 | 77 | 0.47 | 0.82 | 18 | PGE |
| 3 | 93 | 0.42 | 0.78 | 18 | PGE |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5MTD · Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T - crystal… · 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 Q6VT21
- Elsewhere: RCSB PDB 5MTD · PDBe 5MTD · UniProt Q6VT21
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.