MolNFT v1 · #166968 · protein
Crystal structure of antibody 438-B11 dss mutant (CYS98A-100AA) in complex with an uncleaved prefusion optimized (ufo) soluble BG505 trimer and Fab 35O22
6V6W · 35O22 Fab heavy chain: “Crystal structure of antibody 438-B11 dss mutant (CYS98A-100AA) in complex with an uncleaved prefusion…”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.74). MolNFT v1 #166968…
- PDB
- 6V6W
- Type
- protein
- Length
- 2,958 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 35O22 Fab heavy chain; 35O22 Fab light chain; Envelope glycoprotein GP120; B11 dss Fab…
- UniProt
- Q2N0S6, Q2N0S9
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | 35O22 Fab heavy chain | protein | 240 | 3% helix, 43% strand | — |
| E, B | 35O22 Fab light chain | protein | 213 | 6% helix, 46% strand | — |
| G, C | Envelope glycoprotein GP120 | protein | 453 | 14% helix, 34% strand | Q2N0S6 |
| I, F | B11 dss Fab heavy chain | protein | 226 | 4% helix, 46% strand | — |
| J, H | B11 Fab light chain | protein | 213 | 4% helix, 49% strand | — |
| T, K | Envelope glycoprotein GP41 | protein | 134 | 51% helix, 4% strand | Q2N0S9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains G, I, D, T, C, F, A, K, E, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains D, A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains I, D, F, A
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 | 698 | 0.74 | 0.80 | 80 | NAG |
| 2 | 623 | 0.71 | 0.79 | 67 | empty |
| 3 | 160 | 0.70 | 0.89 | 29 | empty |
| 4 | 326 | 0.69 | 0.83 | 62 | empty |
| 5 | 484 | 0.69 | 0.80 | 50 | NAG |
Interfaces
14 interfaces between chains.
- C–K · 2912 Ų buried · 14 hydrogen bonds · protein-protein
- G–T · 2789 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 1903 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 1732 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 1319 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 6V6W · Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an… · the same entry in another collection · chain D against D, 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 Q2N0S9
- Elsewhere: RCSB PDB 6V6W · PDBe 6V6W · UniProt Q2N0S6 · UniProt Q2N0S9
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