MolNFT v1 · #134805 · protein
Crystal structure of 10E8 Fab light chain MUTANT2 against the mper region of the HIV-1 env, in complex with T117V2 epitope scaffold
5TFW · Antibody 10E8 Fab heavy chain: “Crystal structure of 10E8 Fab light chain MUTANT2 against the mper region of the HIV-1 env, in complex with…”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #134805 on GenesisL1: 3D…
- PDB
- 5TFW
- Type
- protein
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 10E8 Fab heavy chain; Antibody 10E8 Fab light chain MUTANT2; 10E8 epitope…
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 233 | 10% helix, 50% strand | — |
| L | Antibody 10E8 Fab light chain MUTANT2 | protein | 213 | 8% helix, 51% strand | — |
| O | 10E8 epitope scaffold T117V2 | protein | 154 | 45% helix, 23% strand | — |
Ligands and binding sites
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 | 615 | 0.70 | 0.78 | 54 | empty |
| 2 | 455 | 0.59 | 0.74 | 49 | PEG, EDO |
| 3 | 117 | 0.44 | 0.78 | 23 | empty |
| 4 | 67 | 0.32 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2145 Ų buried · 18 hydrogen bonds · protein-protein
- H–O · 731 Ų buried · 7 hydrogen bonds · protein-protein
- L–O · 87 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5TFW · Crystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1… · 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 5TFW · PDBe 5TFW
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