Research workbench
Modified BG505 sosip-based immunogen RC1 in complex with the elicited V3-glycan patch bnab 10-1074
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
- 6ORN
- Type
- protein
- Length
- 2,418 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 0.82
Structure
electron microscopy · 4 distinct chains · 14% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, J, Q | RC1 variant of HIV-1 env glycoprotein GP41 | protein | 124 | 50% helix, 2% strand | — |
| G, K, R | RC1 variant of HIV-1 env glycoprotein GP120 | protein | 442 | 11% helix, 33% strand | — |
| A, F, O | 10-1074 antibody Fab heavy chain | protein | 133 | 0% helix, 50% strand | — |
| B, I, P | 10-1074 antibody Fab light chain | protein | 107 | 0% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains G, A, K, F, Q, R, O, C, J
- MAN · alpha-D-mannopyranose · sugar · 20 copies · chains A, B, K, F, I, R, O, P
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, F, O
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 | 1166 | 0.82 | 0.83 | 127 | empty |
| 2 | 85 | 0.74 | 0.96 | 27 | empty |
| 3 | 383 | 0.74 | 0.85 | 58 | NAG |
| 4 | 294 | 0.73 | 0.86 | 44 | empty |
| 5 | 56 | 0.71 | 0.97 | 19 | empty |
Interfaces
21 interfaces between chains.
- J–K · 2296 Ų buried · 5 hydrogen bonds · protein-protein
- Q–R · 2293 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 2270 Ų buried · 5 hydrogen bonds · protein-protein
- F–I · 1069 Ų buried · 7 hydrogen bonds · protein-protein
- O–P · 1059 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ORN · Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch… · the same entry in another collection · chain C against C, 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 6ORN · PDBe 6ORN
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