Research workbench
The crystal structure of rat angiogenin-heparin complex
Analyse The crystal structure of rat angiogenin-heparin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QFJ
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiogenin
- UniProt
- Q5WRG2
- Ligands
- SGN, IDS, ZN
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiogenin | protein | 114 | 25% helix, 37% strand | Q5WRG2 |
| B | Angiogenin | protein | 113 | 25% helix, 39% strand | Q5WRG2 |
Ligands and binding sites
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
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 | 120 | 0.49 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 256 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4QFJ · The crystal structure of rat angiogenin-heparin complex · 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
- Every structure of UniProt Q5WRG2
- Elsewhere: RCSB PDB 4QFJ · PDBe 4QFJ · UniProt Q5WRG2
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