MolNFT v1 · #46718 · protein
The crystal structure of gene product VP1028 from vibrio parahaemolyticus
2OD0 · Hypothetical protein VP1028: “The crystal structure of gene product VP1028 from vibrio parahaemolyticus”. X-ray diffraction, 2 ligands (MG, SO4), 3 pockets (best druggability 0.37). MolNFT v1 #46718 on GenesisL1: 3D structure…
- PDB
- 2OD0
- Type
- protein
- Length
- 205 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein VP1028
- UniProt
- Q87QX1
- Ligands
- MG, SO4
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein VP1028 | protein | 103 | 41% helix, 33% strand | Q87QX1 |
| B | Hypothetical protein VP1028 | protein | 102 | 39% helix, 34% strand | Q87QX1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.37 | 0.76 | 15 | empty |
| 2 | 57 | 0.31 | 0.76 | 13 | empty |
| 3 | 58 | 0.28 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2OD0 · The crystal structure of gene product VP1028 from Vibrio parahaemolyticus · 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 Q87QX1
- Elsewhere: RCSB PDB 2OD0 · PDBe 2OD0 · UniProt Q87QX1
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