MolNFT v1 · #70400 · protein
The X-ray structure of zebrafish RNASE1 from a new crystal form at pH 4.5
3LJD: “The X-ray structure of zebrafish RNASE1 from a new crystal form at pH 4.5”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.40). MolNFT v1 #70400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LJD
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zebrafish RNASE1
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Zebrafish RNASE1 | protein | 126 | 22% helix, 36% strand | — |
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 | 87 | 0.40 | 0.77 | 18 | empty |
| 2 | 65 | 0.35 | 0.77 | 17 | empty |
| 3 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 686 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3LJD · The X-ray structure of zebrafish RNase1 from a new crystal form at pH 4.5 · 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
- Elsewhere: RCSB PDB 3LJD · PDBe 3LJD
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