Research workbench
BG505 MD64 N332-GT5 sosip trimer in complex with BG18-like precursor HMP42 fragmentantigen binding and base-binding RM20A3 fragment antigen binding
Analyse BG505 MD64 N332-GT5 sosip trimer in complex with BG18-like precursor HMP42… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NFC
- Type
- protein
- Length
- 2,584 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Base-binding RM20A3 fragment antigen binding heavy chain; Base-binding RM20A3 fragment…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, J, K | Base-binding RM20A3 fragment antigen binding heavy chain | protein | 123 | 7% helix, 47% strand | — |
| D, M, N | Base-binding RM20A3 fragment antigen binding light chain | protein | 109 | 7% helix, 45% strand | — |
| A, E, F | HIV-1 env BG505 MD64 N332-GT5 sosip GP120 | protein | 432 | 16% helix, 42% strand | — |
| B, G, I | HIV-1 env BG505 MD64 N332-GT5 sosip GP41 | protein | 120 | 60% helix, 8% strand | — |
| H | BG18-like precursor HMP42 fragment antigen binding heavy chain | protein | 126 | 5% helix, 45% strand | — |
| L | BG18-like precursor HMP42 fragment antigen binding light chain | protein | 106 | 6% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains A, F, H, B, E, G, I, K
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.84 | 0.91 | 46 | empty |
| 2 | 294 | 0.72 | 0.85 | 55 | NAG |
| 3 | 304 | 0.71 | 0.84 | 56 | NAG |
| 4 | 328 | 0.71 | 0.84 | 57 | NAG |
| 5 | 71 | 0.66 | 0.94 | 25 | empty |
Interfaces
33 interfaces between chains.
- A–B · 2223 Ų buried · 18 hydrogen bonds · protein-protein
- F–I · 2213 Ų buried · 17 hydrogen bonds · protein-protein
- E–G · 2205 Ų buried · 18 hydrogen bonds · protein-protein
- G–I · 988 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 980 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NFC · BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP42… · 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 6NFC · PDBe 6NFC
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