Research workbench
Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a GP41 mper-derived peptide bearing ala substitutions in a helical conformation
Analyse Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MNZ
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP41 mper-derived peptide; Anti-HIV-1 antibody 13H11 light chain; Anti-HIV-1 antibody…
- UniProt
- Q8TCD0, S6B291
- Ligands
- NA, NH2
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | GP41 mper-derived peptide | protein | 16 | 69% helix, 6% strand | — |
| A | Anti-HIV-1 antibody 13H11 light chain | protein | 220 | 6% helix, 51% strand | Q8TCD0 |
| B | Anti-HIV-1 antibody 13H11 heavy chain | protein | 205 | 10% helix, 53% strand | S6B291 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.58 | 0.91 | 18 | empty |
| 2 | 370 | 0.56 | 0.74 | 49 | empty |
| 3 | 94 | 0.37 | 0.76 | 17 | empty |
| 4 | 129 | 0.37 | 0.73 | 27 | empty |
| 5 | 57 | 0.29 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1521 Ų buried · 6 hydrogen bonds · protein-protein
- P–B · 420 Ų buried · 11 hydrogen bonds · protein-protein
- P–A · 290 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3MNZ · Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41… · the same entry in another collection · chain P against P, 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 S6B291
- Elsewhere: RCSB PDB 3MNZ · PDBe 3MNZ · UniProt Q8TCD0 · UniProt S6B291
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