Research workbench
Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of B12
Analyse Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VN8
- Type
- protein
- Length
- 2,427 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; B12 Fab heavy chain; B12 Fab light chain
- UniProt
- B3UES2, B3UEZ6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 16% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, D, E | Envelope glycoprotein GP160 | protein | 435 | 9% helix, 28% strand | B3UES2 |
| A, B, C | Envelope glycoprotein GP160 | protein | 139 | 58% helix, 3% strand | B3UEZ6 |
| H, F, I | B12 Fab heavy chain | protein | 127 | 7% helix, 32% strand | — |
| L, J, K | B12 Fab light chain | protein | 108 | 3% helix, 31% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 99 copies · chains G, H, D, F, E, I, A, B, C
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains G, L, D, J, E, K
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains G, D, E
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 | 1027 | 0.80 | 0.81 | 83 | empty |
| 2 | 1080 | 0.80 | 0.81 | 98 | empty |
| 3 | 612 | 0.78 | 0.83 | 74 | NAG |
| 4 | 114 | 0.77 | 0.96 | 19 | empty |
| 5 | 112 | 0.77 | 0.96 | 19 | empty |
Interfaces
21 interfaces between chains.
- E–C · 2448 Ų buried · 22 hydrogen bonds · protein-protein
- G–A · 2442 Ų buried · 22 hydrogen bonds · protein-protein
- D–B · 2427 Ų buried · 21 hydrogen bonds · protein-protein
- E–I · 1199 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1187 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 glycan, 36 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5VN8 · Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain… · the same entry in another collection · chain G against G, 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 B3UES2
- Every structure of UniProt B3UEZ6
- Elsewhere: RCSB PDB 5VN8 · PDBe 5VN8 · UniProt B3UES2 · UniProt B3UEZ6
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