Research workbench
Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and 9H/109L
Analyse Crystal structure of BG505-SOSIP.v4.1-GT1-N137A in complex with Fabs 35022 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W6D
- Type
- protein
- Length
- 1,454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.202
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- BG505-SOSIP.v4.1-GT1-N137A gp120; BG505-SOSIP.v4.1-GT1-N137A gp41; 109L FAB light chain…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · resolution 3.202 · 6 distinct chains · 12% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | BG505-SOSIP.v4.1-GT1-N137A gp120 | protein | 447 | 12% helix, 42% strand | — |
| B | BG505-SOSIP.v4.1-GT1-N137A gp41 | protein | 129 | 61% helix, 5% strand | Q2N0S6 |
| L | 109L FAB light chain | protein | 211 | 7% helix, 45% strand | — |
| H | 9H FAB heavy chain | protein | 231 | 1% helix, 50% strand | — |
| D | 35022 FAB heavy chain | protein | 223 | 7% helix, 51% strand | — |
| E | 35022 FAB light chain | protein | 213 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains G, H, B, D, L
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains L, H, D, E, G
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains H, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.66 | 0.94 | 28 | empty |
| 2 | 395 | 0.64 | 0.78 | 41 | empty |
| 3 | 198 | 0.63 | 0.83 | 41 | NAG |
| 4 | 299 | 0.63 | 0.80 | 39 | empty |
| 5 | 525 | 0.60 | 0.74 | 62 | empty |
Interfaces
8 interfaces between chains.
- G–B · 2666 Ų buried · 24 hydrogen bonds · protein-protein
- L–H · 2077 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1618 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 409 Ų buried · 5 hydrogen bonds · protein-protein
- G–D · 343 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan, 1 isopeptide (disulfide, N-glycosylation, isopeptide).
Compared structures
- 5W6D · Crystal structure of BG505-SOSIP.V4.1-GT1-N137A in complex with fabs 35022 and 9H/109L · the same entry in another collection · chain B against B, 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 Q2N0S6
- Elsewhere: RCSB PDB 5W6D · PDBe 5W6D · UniProt Q2N0S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.