MolNFT v1 · #55139 · protein
Structure of an amidohydrolase from chromobacterium violaceum (efi target efi-500202) with bound mn, AMP and phosphate.
2YB1: “Structure of an amidohydrolase from chromobacterium violaceum (efi target efi-500202) with bound mn, AMP and…”. X-ray diffraction, 3 ligands (AMP, MN, PO4), 1 pocket (best druggability 0.65). MolNFT v1 #55139 on GenesisL1: 3D…
- PDB
- 2YB1
- Type
- protein
- Length
- 284 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidohydrolase
- UniProt
- Q7NXD4
- Ligands
- AMP, MN, PO4
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidohydrolase | protein | 284 | 42% helix, 16% strand | Q7NXD4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- PO4 · Phosphate ion · ion · chains A
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 | 406 | 0.65 | 0.79 | 42 | MN, AMP, PO4 |
Compared structures
- 2YB1 · Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7NXD4 · AlphaFold monomer V2.0 prediction for 3',5'-nucleoside bisphosphate phosphatase (Q7NXD4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q7NXD4
- Elsewhere: RCSB PDB 2YB1 · PDBe 2YB1 · UniProt Q7NXD4
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