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The crystal structure of an amidohydrolase from mycoplasma synoviae with zn ion bound
Analyse The crystal structure of an amidohydrolase from mycoplasma synoviae with zn ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OVG
- Type
- protein
- Length
- 2,106 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase
- UniProt
- Q4A724
- Ligands
- ZN, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Amidohydrolase | protein | 351 | 48% helix, 17% strand | Q4A724 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.79 | 0.80 | 88 | empty |
| 2 | 757 | 0.77 | 0.81 | 62 | empty |
| 3 | 765 | 0.77 | 0.81 | 60 | empty |
| 4 | 651 | 0.72 | 0.78 | 46 | empty |
| 5 | 641 | 0.71 | 0.78 | 46 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1050 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 1037 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1027 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 959 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 958 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered, carboxylation).
Compared structures
- 3OVG · The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound · the same entry in another collection · chain C against C, TM-score 1.00
- Q4A724 · AlphaFold monomer V2.0 prediction for phospho-furanose lactonase (Q4A724) · a predicted model of the same protein · 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 Q4A724
- Elsewhere: RCSB PDB 3OVG · PDBe 3OVG · UniProt Q4A724
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