MolNFT v1 · #74394 · protein
The crystal structure of an amidohydrolase from mycoplasma synoviae with zn ion bound
3OVG: “The crystal structure of an amidohydrolase from mycoplasma synoviae with zn ion bound”. X-ray diffraction, 2 ligands (ZN, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #74394 on GenesisL1: 3D structure, binding sites and…
- 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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