MolNFT v1 · #188772 · protein
Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24
7UCF · Envelope glycoprotein GP41: “Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 18 pockets (best druggability 0.71). MolNFT v1…
- PDB
- 7UCF
- Type
- protein
- Length
- 1,450 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; BG24 Fab heavy chain; BG24 light chain; Envelope glycoprotein…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Envelope glycoprotein GP41 | protein | 137 | 48% helix, 5% strand | Q2N0S6 |
| D | BG24 Fab heavy chain | protein | 220 | 7% helix, 45% strand | — |
| E | BG24 light chain | protein | 202 | 3% helix, 44% strand | — |
| G | Envelope glycoprotein GP120 | protein | 451 | 12% helix, 39% strand | Q2N0S6 |
| H | 10-1074 Fab heavy chain | protein | 229 | 7% helix, 53% strand | — |
| L | 10-1074 Fab light chain | protein | 211 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains B, E, G, H, D
- MAN · alpha-D-mannopyranose · sugar · 22 copies · chains E, H, L, D
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains H
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains B, G
- GAL · beta-D-galactopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.71 | 0.85 | 44 | empty |
| 2 | 311 | 0.69 | 0.84 | 47 | empty |
| 3 | 415 | 0.68 | 0.80 | 69 | NAG |
| 4 | 236 | 0.67 | 0.84 | 27 | empty |
| 5 | 199 | 0.53 | 0.78 | 29 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2846 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1988 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1830 Ų buried · 19 hydrogen bonds · protein-protein
- D–G · 950 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 375 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 18 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7UCF · Structure of the BG505 SOSIP.664 trimer in complex with neutralizing antibody Fab… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 7UCF · PDBe 7UCF · UniProt Q2N0S6
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