Research workbench
Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan patch antibody AB275MUR
Analyse Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ORQ
- Type
- protein
- Length
- 2,430 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RC1 variant of HIV-1 env glycoprotein GP41; RC1 variant of HIV-1 env glycoprotein GP120…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 16% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | RC1 variant of HIV-1 env glycoprotein GP41 | protein | 124 | 52% helix, 6% strand | — |
| B, G, I | RC1 variant of HIV-1 env glycoprotein GP120 | protein | 453 | 14% helix, 29% strand | — |
| D, H, J | AB275MUR antibody Fab heavy chain | protein | 122 | 0% helix, 16% strand | — |
| E, K, L | AB275MUR antibody Fab light chain | protein | 111 | 3% helix, 22% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 73 copies · chains B, G, I, A, C, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains G
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.87 | 0.88 | 122 | empty |
| 2 | 1003 | 0.82 | 0.83 | 152 | empty |
| 3 | 197 | 0.77 | 0.92 | 37 | empty |
| 4 | 92 | 0.76 | 0.97 | 28 | empty |
| 5 | 354 | 0.75 | 0.85 | 65 | NAG |
Interfaces
21 interfaces between chains.
- A–B · 2530 Ų buried · 6 hydrogen bonds · protein-protein
- F–I · 2515 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 2492 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 888 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 853 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 glycan, 27 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6ORQ · Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch… · 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 6ORQ · PDBe 6ORQ
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