MolNFT v1 · #116975 · protein
Context-independent anti-hypusine antibody FABHPU98 in complex with deoxyhypusine
5DUB · Fab HPU98 heavy chain: “Context-independent anti-hypusine antibody FABHPU98 in complex with deoxyhypusine”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.73). MolNFT v1 #116975 on GenesisL1: 3D structure, binding…
- PDB
- 5DUB
- Type
- protein
- Length
- 845 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab HPU98 heavy chain; Fab HPU98 light chain; Peptide: gly-5GG-gly-ala
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab HPU98 heavy chain | protein | 209 | 6% helix, 56% strand | — |
| B | Fab HPU98 light chain | protein | 214 | 7% helix, 53% strand | — |
| H | Fab HPU98 heavy chain | protein | 207 | 6% helix, 52% strand | — |
| L | Fab HPU98 light chain | protein | 211 | 5% helix, 54% strand | — |
| P | Peptide: gly-5GG-gly-ala | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 13 copies · chains A, L, B, H, P
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.73 | 0.81 | 68 | EDO, SO4 |
| 2 | 318 | 0.60 | 0.78 | 37 | EDO |
| 3 | 400 | 0.58 | 0.75 | 46 | EDO |
| 4 | 80 | 0.54 | 0.86 | 23 | EDO, SO4 |
| 5 | 122 | 0.50 | 0.80 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1960 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1880 Ų buried · 24 hydrogen bonds · protein-protein
- A–H · 494 Ų buried · 12 hydrogen bonds · protein-protein
- B–H · 410 Ų buried · 8 hydrogen bonds · protein-protein
- H–P · 227 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 modified (disulfide, cyclization, nonstandard).
Compared structures
- 5DUB · Context-independent anti-hypusine antibody FabHpu98 in complex with deoxyhypusine · 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 5DUB · PDBe 5DUB
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