Research workbench
Crystal structure of Fab of human mab 2909 specific for quaternary neutralizing epitope of HIV-1 GP120
Analyse Crystal structure of Fab of human mab 2909 specific for quaternary neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q6F
- Type
- protein
- Length
- 2,643 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of Fab of human mab 2909; Heavy chain of Fab of human mab 2909
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Light chain of Fab of human mab 2909 | protein | 212 | 8% helix, 50% strand | — |
| B, D, F, H | Heavy chain of Fab of human mab 2909 | protein | 228 | 8% helix, 50% strand | — |
| J | Heavy chain of Fab of human mab 2909 | protein | 230 | 8% helix, 51% strand | — |
| L | Heavy chain of Fab of human mab 2909 | protein | 229 | 8% helix, 52% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains G, H, C, D, I, J, A, B, E, F, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.75 | 0.88 | 38 | empty |
| 2 | 319 | 0.72 | 0.85 | 36 | empty |
| 3 | 506 | 0.71 | 0.80 | 60 | empty |
| 4 | 676 | 0.66 | 0.75 | 62 | empty |
| 5 | 313 | 0.57 | 0.77 | 40 | empty |
Interfaces
24 interfaces between chains.
- G–H · 1863 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 1861 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1846 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1843 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 1843 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 12 modified (disulfide, sulfation).
Compared structures
- 3Q6F · Crystal structure of Fab of human mAb 2909 specific for quaternary neutralizing epitope… · 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
- Elsewhere: RCSB PDB 3Q6F · PDBe 3Q6F
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.