Research workbench
Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5
Analyse Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8T5C
- Type
- protein
- Length
- 1,651 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.7
- Source
- Camelus bactrianus; Homo sapiens; Lassa virus Josiah
- Molecule
- Glycoprotein G1; Glycoprotein G2; D5 nanobody; 8.11G Heavy Chain; 8.11G Light Chain
- UniProt
- P08669
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · resolution 4.7 · 6 distinct chains · 15% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | Glycoprotein G1 | protein | 202 | 18% helix, 17% strand | P08669 |
| b, a, c | Glycoprotein G2 | protein | 159 | 41% helix, 10% strand | P08669 |
| A | Glycoprotein G1 | protein | 198 | 15% helix, 15% strand | P08669 |
| D | D5 nanobody | protein | 116 | 3% helix, 37% strand | — |
| H, E | 8.11G Heavy Chain | protein | 119 | 3% helix, 37% strand | — |
| L, I | 8.11G Light Chain | protein | 109 | 0% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 copies · chains B, b, I, D, E, A, a, L, H, C, c
- MAN · alpha-D-mannopyranose · sugar · 26 copies · chains b, E, I, B, a, H, L, A, c, C
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains b, I, B, E, a, L, A, H, C
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 | 956 | 0.90 | 0.93 | 138 | empty |
| 2 | 1126 | 0.84 | 0.84 | 108 | empty |
| 3 | 1120 | 0.78 | 0.80 | 96 | empty |
| 4 | 731 | 0.78 | 0.82 | 71 | empty |
| 5 | 246 | 0.73 | 0.87 | 51 | empty |
Interfaces
27 interfaces between chains.
- C–c · 2978 Ų buried · 41 hydrogen bonds · protein-protein
- B–b · 2813 Ų buried · 28 hydrogen bonds · protein-protein
- A–a · 2701 Ų buried · 34 hydrogen bonds · protein-protein
- H–L · 897 Ų buried · 6 hydrogen bonds · protein-protein
- E–I · 876 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 glycan, 26 disulfide (N-glycosylation, disulfide).
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 P08669
- Elsewhere: RCSB PDB 8T5C · PDBe 8T5C · UniProt P08669
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