MolNFT v1 · #116887 · protein
Context-independent anti-hypusine antibody FABHPU24 in complex with hypusine
5DRN · Fab HPU24 heavy chain: “Context-independent anti-hypusine antibody FABHPU24 in complex with hypusine”. X-ray diffraction, 1 ligand (5CT), 5 pockets (best druggability 0.61). MolNFT v1 #116887 on GenesisL1: 3D structure, binding…
- PDB
- 5DRN
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab HPU24 heavy chain; Fab HPU24 light chain
- Ligands
- 5CT
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab HPU24 heavy chain | protein | 216 | 6% helix, 53% strand | — |
| B | Fab HPU24 light chain | protein | 215 | 9% helix, 52% strand | — |
| H | Fab HPU24 heavy chain | protein | 213 | 7% helix, 54% strand | — |
| L | Fab HPU24 light chain | protein | 213 | 8% helix, 52% strand | — |
Ligands and binding sites
- 5CT · Hypusine · ligand · 2 copies · chains A, B, H, L
- GOL · Glycerol · additive · 4 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.61 | 0.75 | 55 | GOL |
| 2 | 482 | 0.60 | 0.75 | 52 | GOL |
| 3 | 251 | 0.50 | 0.75 | 43 | empty |
| 4 | 77 | 0.31 | 0.74 | 19 | empty |
| 5 | 62 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1825 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1777 Ų buried · 16 hydrogen bonds · protein-protein
- B–L · 301 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5DRN · Context-independent anti-hypusine antibody FabHpu24 in complex with hypusine · 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 5DRN · PDBe 5DRN
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