Research workbench
Cryo-EM structure of a BG505 env-SCD4-17B-8ANC195 complex
Analyse Cryo-EM structure of a BG505 env-SCD4-17B-8ANC195 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THR
- Type
- protein
- Length
- 3,171 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 sosip GP41; BG505 sosip GP120; T-cell surface glycoprotein CD4; 17B Fab vl domain…
- UniProt
- Q2N0S6, P01730
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 14% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BG505 sosip GP41 | protein | 124 | 55% helix, 0% strand | Q2N0S6 |
| B, C | BG505 sosip GP41 | protein | 123 | 55% helix, 1% strand | Q2N0S6 |
| D, E, F | BG505 sosip GP120 | protein | 364 | 12% helix, 25% strand | Q2N0S6 |
| G, H | T-cell surface glycoprotein CD4 | protein | 98 | 0% helix, 35% strand | P01730 |
| I | T-cell surface glycoprotein CD4 | protein | 97 | 0% helix, 33% strand | P01730 |
| J, K, L | 17B Fab vl domain | protein | 107 | 0% helix, 31% strand | — |
| M, N, O | 17B Fab vh domain | protein | 127 | 2% helix, 42% strand | — |
| P, R, T | 8ANC195 G52K5 vh domain | protein | 131 | 2% helix, 34% strand | — |
| Q, S, U | 8ANC195 G52K5 vl domain | protein | 107 | 0% helix, 34% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains D, T, G, E, R, F, P
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains T, R, P
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains T, R, P
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 | 908 | 0.82 | 0.84 | 110 | empty |
| 2 | 250 | 0.77 | 0.90 | 41 | empty |
| 3 | 244 | 0.75 | 0.89 | 36 | empty |
| 4 | 211 | 0.75 | 0.90 | 37 | empty |
| 5 | 55 | 0.72 | 0.98 | 17 | empty |
Interfaces
39 interfaces between chains.
- B–D · 2134 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 2040 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 2031 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 1224 Ų buried · 25 hydrogen bonds · protein-protein
- E–H · 1115 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 10 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5THR · Cryo-EM structure of a BG505 Env-sCD4-17b-8ANC195 complex · 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 Q2N0S6
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 5THR · PDBe 5THR · UniProt Q2N0S6 · UniProt P01730
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