MolNFT v1 · #134240 · protein
Crystal structure of the complex of 10E8 Fab light chain MUTANT1 and T117V2 HIV-1 mper scaffold
5SY8 · 10E8 Fab heavy chain: “Crystal structure of the complex of 10E8 Fab light chain MUTANT1 and T117V2 HIV-1 mper scaffold”. X-ray diffraction, 4 pockets (best druggability 0.66). MolNFT v1 #134240 on GenesisL1: 3D structure, binding…
- PDB
- 5SY8
- Type
- protein
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 10E8 Fab heavy chain; 10E8 Fab light chain; 10E8 epitope scaffold T117V2
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 10E8 Fab heavy chain | protein | 234 | 9% helix, 52% strand | — |
| L | 10E8 Fab light chain | protein | 212 | 8% helix, 50% strand | — |
| O | 10E8 epitope scaffold T117V2 | protein | 155 | 45% helix, 23% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains L, H, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.66 | 0.78 | 45 | GOL |
| 2 | 368 | 0.56 | 0.74 | 43 | empty |
| 3 | 52 | 0.42 | 0.83 | 19 | empty |
| 4 | 111 | 0.41 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2186 Ų buried · 22 hydrogen bonds · protein-protein
- H–O · 779 Ų buried · 7 hydrogen bonds · protein-protein
- L–O · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5SY8 · Crystal structure of the complex of 10E8 Fab light chain mutant1 and T117v2 HIV-1 MPER… · the same entry in another collection · chain H against H, 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 5SY8 · PDBe 5SY8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.