Research workbench
Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment
Analyse Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MNV
- Type
- protein
- Length
- 857 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HIV-1 antibody 13H11 light chain; Anti-HIV-1 antibody 13H11 heavy chain
- UniProt
- Q8TCD0, Q6N089
- Ligands
- SO4, CL, NO3
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-HIV-1 antibody 13H11 light chain | protein | 221 | 6% helix, 52% strand | Q8TCD0 |
| B | Anti-HIV-1 antibody 13H11 heavy chain | protein | 208 | 10% helix, 51% strand | Q6N089 |
| C | Anti-HIV-1 antibody 13H11 light chain | protein | 220 | 5% helix, 52% strand | Q8TCD0 |
| D | Anti-HIV-1 antibody 13H11 heavy chain | protein | 208 | 10% helix, 50% strand | Q6N089 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B, C
- CL · Chloride ion · ion · chains B
- NO3 · Nitrate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.71 | 0.77 | 85 | SO4 |
| 2 | 132 | 0.62 | 0.86 | 24 | empty |
| 3 | 413 | 0.58 | 0.75 | 57 | empty |
| 4 | 56 | 0.54 | 0.89 | 21 | empty |
| 5 | 276 | 0.49 | 0.73 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1636 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1618 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 739 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 414 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 308 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3MNV · Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment · 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
- Every structure of UniProt Q8TCD0
- Every structure of UniProt Q6N089
- Elsewhere: RCSB PDB 3MNV · PDBe 3MNV · UniProt Q8TCD0 · UniProt Q6N089
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