Research workbench
BG505 MD64 N332-GT5 sosip trimer in complex with BG18-like precursor HMP1 fragmentantigen binding and base-binding RM20A3 fragment antigen binding
Analyse BG505 MD64 N332-GT5 sosip trimer in complex with BG18-like precursor HMP1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NF5
- Type
- protein
- Length
- 3,048 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 env BG505 MD64 N332-GT5 sosip GP120; HIV-1 env BG505 MD64 N332-GT5 sosip GP41…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, J | HIV-1 env BG505 MD64 N332-GT5 sosip GP120 | protein | 436 | 15% helix, 44% strand | — |
| B, D, M | HIV-1 env BG505 MD64 N332-GT5 sosip GP41 | protein | 122 | 64% helix, 7% strand | — |
| H, E, O | BG18-like precursor HMP1 fragment antigen binding heavy chain | protein | 128 | 9% helix, 49% strand | — |
| L, F, P | BG18-like precursor HMP1 fragment antigen binding light chain | protein | 99 | 3% helix, 45% strand | — |
| K, G, Q | Base-binding RM20A3 fragment antigen binding heavy chain | protein | 123 | 7% helix, 48% strand | — |
| N, I, R | Base-binding RM20A3 fragment antigen binding light chain | protein | 108 | 6% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 75 copies · chains A, H, B, C, E, D, J, O, M
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, H, C, E, J, O
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains H, E, 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 | 386 | 0.84 | 0.93 | 43 | empty |
| 2 | 323 | 0.70 | 0.83 | 46 | NAG |
| 3 | 297 | 0.70 | 0.84 | 47 | NAG |
| 4 | 315 | 0.70 | 0.83 | 50 | NAG |
| 5 | 805 | 0.68 | 0.75 | 59 | empty |
Interfaces
39 interfaces between chains.
- A–B · 2377 Ų buried · 21 hydrogen bonds · protein-protein
- J–M · 2373 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2368 Ų buried · 21 hydrogen bonds · protein-protein
- B–M · 1033 Ų buried · 6 hydrogen bonds · protein-protein
- D–M · 1033 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NF5 · BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragmentantigen… · the same entry in another collection · chain N against N, 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 6NF5 · PDBe 6NF5
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