MolNFT v1 · #8424 · protein
Crystal structure of human angiogenin in complex with Fab fragment of its monoclonal antibody mab 26-2F
1H0D · Antibody Fab fragment, light chain: “Crystal structure of human angiogenin in complex with Fab fragment of its monoclonal antibody mab 26-2F”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.57). MolNFT v1 #8424 on…
- PDB
- 1H0D
- Type
- protein
- Length
- 562 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment, light chain; Antibody Fab fragment, heavy chain; Angiogenin
- UniProt
- P03950
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment, light chain | protein | 216 | 6% helix, 52% strand | — |
| B | Antibody Fab fragment, heavy chain | protein | 223 | 7% helix, 48% strand | — |
| C | Angiogenin | protein | 123 | 25% helix, 29% strand | P03950 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.57 | 0.75 | 45 | GOL |
| 2 | 167 | 0.44 | 0.74 | 33 | empty |
| 3 | 102 | 0.40 | 0.76 | 23 | empty |
| 4 | 119 | 0.38 | 0.74 | 21 | empty |
| 5 | 80 | 0.32 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1972 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 466 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 325 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 1H0D · Crystal structure of Human Angiogenin in complex with Fab fragment of its monoclonal… · the same entry in another collection · chain A against A, TM-score 1.00
- P03950 · AlphaFold monomer V2.0 prediction for angiogenin (P03950) · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P03950
- Elsewhere: RCSB PDB 1H0D · PDBe 1H0D · UniProt P03950
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