Research workbench
BG505 sosip in complex with SCD4, 17B, 8ANC195
Analyse BG505 sosip in complex with SCD4, 17B, 8ANC195 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CM3
- Type
- protein
- Length
- 3,177 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; T-cell surface glycoprotein CD4; 17B Fab light chain; 17B…
- UniProt
- Q2N0S7, Q2N0S5, P01730
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein GP160 | protein | 118 | 62% helix, 2% strand | Q2N0S7 |
| D, E, F | Envelope glycoprotein GP160 | protein | 372 | 14% helix, 27% strand | Q2N0S5 |
| G, H, I | T-cell surface glycoprotein CD4 | protein | 97 | 6% helix, 42% strand | P01730 |
| J, L, N | 17B Fab light chain | protein | 107 | 0% helix, 38% strand | — |
| K, M, O | 17B Fab heavy chain | protein | 127 | 5% helix, 49% strand | — |
| P, R, T | 8ANC195 Fab heavy chain | protein | 131 | 2% helix, 45% strand | — |
| Q, S, U | 8ANC195 Fab light chain | protein | 107 | 0% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 48 copies · chains A, S, R, B, Q, P, C, U, T, D, G, E, I, F, H
- MAN · alpha-D-mannopyranose · sugar · 33 copies · chains P, D, R, E, T, F
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains P, R, T
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 | 1107 | 0.85 | 0.86 | 129 | empty |
| 2 | 765 | 0.71 | 0.77 | 84 | NAG |
| 3 | 51 | 0.70 | 0.99 | 27 | empty |
| 4 | 52 | 0.70 | 0.97 | 18 | empty |
| 5 | 72 | 0.69 | 0.94 | 25 | empty |
Interfaces
36 interfaces between chains.
- A–E · 2100 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 2094 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 2068 Ų buried · 11 hydrogen bonds · protein-protein
- D–G · 1175 Ų buried · 15 hydrogen bonds · protein-protein
- E–I · 1175 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 36 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 6CM3 · BG505 SOSIP in complex with sCD4, 17b, 8ANC195 · the same entry in another collection · chain U against U, 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 Q2N0S7
- Every structure of UniProt Q2N0S5
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 6CM3 · PDBe 6CM3 · UniProt Q2N0S7 · UniProt Q2N0S5 · UniProt P01730
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