Research workbench
B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3- targeting antibody 10-1074
Analyse B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3- targeting… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKP
- Type
- protein
- Length
- 2,660 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP41; Envelope glycoprotein GP120; 10-1074 heavy CHAIN,10-1074…
- UniProt
- B3UEZ6, B3UES2, S6B291, Q8N5F4, P01834
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 10% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Envelope glycoprotein GP41 | protein | 118 | 51% helix, 6% strand | B3UEZ6 |
| D, F | Envelope glycoprotein GP120 | protein | 456 | 7% helix, 30% strand | B3UES2 |
| E | Envelope glycoprotein GP120 | protein | 455 | 10% helix, 32% strand | B3UES2 |
| K | 10-1074 heavy CHAIN,10-1074 heavy chain | protein | 133 | 7% helix, 44% strand | S6B291 |
| L | 10-1074 light CHAIN,10-1074 light chain | protein | 101 | 3% helix, 26% strand | Q8N5F4 |
| M, O, Q | SF12 heavy CHAIN,SF12 heavy chain | protein | 131 | 5% helix, 44% strand | S6B291 |
| N, P, R | SF12 light CHAIN,SF12 light chain | protein | 104 | 0% helix, 46% strand | P01834 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 95 copies · chains D, M, E, O, K, L, F, Q, A, B, C
- MAN · alpha-D-mannopyranose · sugar · 46 copies · chains M, D, N, P, O, K, L, Q, R, E, F
- BMA · beta-D-mannopyranose · sugar · 16 copies · chains M, D, O, E, K, Q, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.81 | 0.86 | 80 | empty |
| 2 | 850 | 0.77 | 0.80 | 93 | NAG |
| 3 | 884 | 0.77 | 0.80 | 101 | NAG |
| 4 | 827 | 0.76 | 0.80 | 94 | NAG |
| 5 | 69 | 0.73 | 0.97 | 18 | empty |
Interfaces
24 interfaces between chains.
- C–F · 2718 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 2715 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2712 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1059 Ų buried · 5 hydrogen bonds · protein-protein
- O–P · 747 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 67 glycan, 27 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6OKP · B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody… · the same entry in another collection · chain R against R, 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 B3UEZ6
- Every structure of UniProt B3UES2
- Every structure of UniProt S6B291
- Every structure of UniProt Q8N5F4
- Every structure of UniProt P01834
- Elsewhere: RCSB PDB 6OKP · PDBe 6OKP · UniProt B3UEZ6 · UniProt B3UES2 · UniProt S6B291 · UniProt Q8N5F4 · UniProt P01834
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