Research workbench
Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan patch antibody AB874NHP
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
- 6ORO
- Type
- protein
- Length
- 2,415 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, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 12% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | RC1 variant of HIV-1 env glycoprotein GP41 | protein | 124 | 45% helix, 6% strand | — |
| B, G, I | RC1 variant of HIV-1 env glycoprotein GP120 | protein | 449 | 9% helix, 31% strand | — |
| D, H, J | AB874NHP antibody Fab heavy chain | protein | 124 | 0% helix, 27% strand | — |
| E, K, L | AB874NHP antibody Fab light chain | protein | 108 | 0% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains B, G, I, A, C, F
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains B, D, G, H, I, J
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains B, G, 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 | 354 | 0.83 | 0.92 | 48 | empty |
| 2 | 988 | 0.69 | 0.74 | 78 | empty |
| 3 | 741 | 0.68 | 0.76 | 69 | empty |
| 4 | 331 | 0.65 | 0.80 | 48 | empty |
| 5 | 160 | 0.65 | 0.85 | 29 | NAG |
Interfaces
21 interfaces between chains.
- A–B · 2584 Ų buried · 11 hydrogen bonds · protein-protein
- F–I · 2578 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 2577 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 859 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 853 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 33 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6ORO · 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 6ORO · PDBe 6ORO
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