MolNFT v1 · #134376 · protein
Crystal structure of 10E8 Fab light chain MUTANT3, against the mper region of the HIV-1 env, in complex with the mper epitope scaffold T117V2
5T29 · Antibody 10E8 Fab heavy chain: “Crystal structure of 10E8 Fab light chain MUTANT3, against the mper region of the HIV-1 env, in complex with…”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.67). MolNFT v1 #134376…
- PDB
- 5T29
- Type
- protein
- Length
- 589 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; 10E8 epitope scaffold T117V2
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 232 | 9% helix, 52% strand | — |
| L | Antibody 10E8 Fab light chain | protein | 211 | 8% helix, 51% strand | — |
| O | 10E8 epitope scaffold T117V2 | protein | 146 | 42% helix, 24% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.67 | 0.77 | 48 | empty |
| 2 | 535 | 0.60 | 0.74 | 55 | empty |
| 3 | 147 | 0.58 | 0.82 | 21 | empty |
| 4 | 87 | 0.45 | 0.80 | 17 | empty |
| 5 | 90 | 0.35 | 0.74 | 28 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2097 Ų buried · 19 hydrogen bonds · protein-protein
- H–O · 771 Ų buried · 7 hydrogen bonds · protein-protein
- L–O · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5T29 · Crystal structure of 10E8 Fab light chain mutant3, 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 5T29 · PDBe 5T29
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