Research workbench
BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab
Analyse BG505 SOSIP.V5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLR
- Type
- protein
- Length
- 2,611 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; BG505 SOSIPV5.2 GP41; PGT122 Fab heavy chain; PGT122 Fab…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, G | Envelope glycoprotein GP120 | protein | 430 | 13% helix, 44% strand | Q2N0S6 |
| B | BG505 SOSIPV5.2 GP41 | protein | 128 | 56% helix, 4% strand | Q2N0S6 |
| J, I | BG505 SOSIPV5.2 GP41 | protein | 122 | 62% helix, 4% strand | Q2N0S6 |
| C, D, E | PGT122 Fab heavy chain | protein | 132 | 7% helix, 55% strand | — |
| L, K, M | PGT122 Fab light chain | protein | 106 | 3% helix, 43% strand | — |
| F | RM20E1 Fab heavy chain | protein | 123 | 5% helix, 51% strand | — |
| N | RM20E1 Fab kappa chain | protein | 112 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 62 copies · chains A, C, L, B, H, D, K, J, G, E, M, I
- MAN · alpha-D-mannopyranose · sugar · 19 copies · chains C, L, H, D, K, G, E, M
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains C, 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 | 463 | 0.81 | 0.88 | 67 | empty |
| 2 | 79 | 0.75 | 0.97 | 26 | empty |
| 3 | 342 | 0.74 | 0.85 | 61 | NAG |
| 4 | 851 | 0.74 | 0.78 | 93 | empty |
| 5 | 64 | 0.72 | 0.98 | 26 | empty |
Interfaces
26 interfaces between chains.
- H–J · 2388 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2251 Ų buried · 25 hydrogen bonds · protein-protein
- G–I · 2198 Ų buried · 23 hydrogen bonds · protein-protein
- C–L · 1168 Ų buried · 17 hydrogen bonds · protein-protein
- D–K · 1117 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 31 glycan (disulfide, N-glycosylation).
Compared structures
- 6VLR · BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab · the same entry in another collection · chain J against J, 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 6VLR · PDBe 6VLR · UniProt Q2N0S6
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