MolNFT v1 · #118750 · protein
S1 nuclease from aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate
5FBF · Nuclease S1: “S1 nuclease from aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate”. X-ray diffraction, 4 ligands (DCM, NAG, ZN), 1 pocket (best druggability 0.33). MolNFT v1 #118750 on GenesisL1…
- PDB
- 5FBF
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclease S1
- EC
- 3.1.30.1
- UniProt
- P24021
- Ligands
- DCM, NAG, ZN, NA
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclease S1 (EC 3.1.30.1) | protein | 267 | 64% helix, 4% strand | P24021 |
Ligands and binding sites
- DCM · 2'-deoxycytidine-5'-monophosphate · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.33 | 0.77 | 19 | DCM |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P24021
- Elsewhere: RCSB PDB 5FBF · PDBe 5FBF · UniProt P24021
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