MolNFT v1 · #134480 · protein
Crystal structure of the complex of 10E8 Fab light chain MUTANT5 and T117V2 HIV-1 mper scaffold
5T5B · Antibody 10E8 Fab heavy chain: “Crystal structure of the complex of 10E8 Fab light chain MUTANT5 and T117V2 HIV-1 mper scaffold”. X-ray diffraction, 11 pockets (best druggability 0.69). MolNFT v1 #134480 on GenesisL1: 3D structure…
- PDB
- 5T5B
- Type
- protein
- Length
- 1,135 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 10E8 Fab heavy chain; Antibody 10E8 Fab light chain mutated; 10E8 epitope…
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody 10E8 Fab heavy chain | protein | 206 | 6% helix, 50% strand | — |
| L | Antibody 10E8 Fab light chain mutated | protein | 212 | 8% helix, 50% strand | — |
| A | Antibody 10E8 Fab heavy chain | protein | 205 | 7% helix, 50% strand | — |
| B | Antibody 10E8 Fab light chain mutated | protein | 210 | 8% helix, 50% strand | — |
| O | 10E8 epitope scaffold T117V2 | protein | 150 | 45% helix, 24% strand | — |
| E | 10E8 epitope scaffold T117V2 | protein | 152 | 43% helix, 24% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains H, L, A, O, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.69 | 0.78 | 48 | GOL |
| 2 | 513 | 0.64 | 0.76 | 48 | GOL |
| 3 | 334 | 0.53 | 0.74 | 46 | empty |
| 4 | 285 | 0.50 | 0.73 | 53 | empty |
| 5 | 200 | 0.47 | 0.75 | 34 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1903 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1884 Ų buried · 14 hydrogen bonds · protein-protein
- A–O · 755 Ų buried · 8 hydrogen bonds · protein-protein
- H–E · 751 Ų buried · 6 hydrogen bonds · protein-protein
- H–A · 434 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5T5B · Crystal structure of the complex of 10E8 Fab light chain MUTANT5 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 5T5B · PDBe 5T5B
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