Research workbench
HIV env BG505 sosip with polyclonal fabs from immunized rabbit #3417 post-BOOST#1
Analyse HIV env BG505 sosip with polyclonal fabs from immunized rabbit #3417… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DID
- Type
- protein
- Length
- 3,009 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Monoclonal antibody 10A light chain; Monoclonal antibody 10A…
- UniProt
- Q2N0S6, Q2N0S7, P01840, A0A1Y1B8B1
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | Envelope glycoprotein GP160 | protein | 444 | 15% helix, 38% strand | Q2N0S6 |
| B, I, J | Envelope glycoprotein GP160 | protein | 129 | 63% helix, 2% strand | Q2N0S7 |
| C, E, H | Monoclonal antibody 10A light chain | protein | 217 | 8% helix, 53% strand | P01840 |
| D, K, L | Monoclonal antibody 10A heavy chain | protein | 213 | 4% helix, 53% strand | A0A1Y1B8B1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, B, H, F, I, C, G, J, E
- MAN · alpha-D-mannopyranose · sugar · 39 copies · chains A, F, G
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains A, F, G
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 | 349 | 0.82 | 0.91 | 48 | empty |
| 2 | 424 | 0.77 | 0.85 | 75 | NAG |
| 3 | 357 | 0.77 | 0.86 | 60 | NAG |
| 4 | 355 | 0.76 | 0.86 | 61 | NAG |
| 5 | 922 | 0.74 | 0.77 | 108 | empty |
Interfaces
21 interfaces between chains.
- F–I · 2609 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2606 Ų buried · 30 hydrogen bonds · protein-protein
- G–J · 2602 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 1723 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 54 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6DID · HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q2N0S7
- Every structure of UniProt P01840
- Every structure of UniProt A0A1Y1B8B1
- Elsewhere: RCSB PDB 6DID · PDBe 6DID · UniProt Q2N0S6 · UniProt Q2N0S7 · UniProt P01840 · UniProt A0A1Y1B8B1
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