Research workbench
BG505 SOSIP.V5.2(7S) in complex with the monoclonal antibodies RH.33172 MAB.1 and RM19R
Analyse BG505 SOSIP.V5.2(7S) in complex with the monoclonal antibodies RH.33172 MAB.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEP
- Type
- protein
- Length
- 2,596 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RM19R mab light chain; RM19R mab heavy chain; BG505 SOSIPV5.2(7S) - GP120; RH.33172 MAB.1…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, K | RM19R mab light chain | protein | 105 | 0% helix, 49% strand | — |
| I, M, N | RM19R mab heavy chain | protein | 118 | 11% helix, 54% strand | — |
| A | BG505 SOSIPV5.2(7S) - GP120 | protein | 440 | 15% helix, 43% strand | — |
| B, E, F | BG505 SOSIPV5.2(7S) - GP120 | protein | 123 | 62% helix, 7% strand | — |
| H | RH.33172 MAB.1 heavy chain | protein | 128 | 7% helix, 48% strand | — |
| L | RH.33172 MAB.1 light chain | protein | 107 | 3% helix, 45% strand | — |
| J | RM19R mab light chain | protein | 104 | 0% helix, 45% strand | — |
| C | BG505 SOSIPV5.2(7S) - GP120 | protein | 441 | 16% helix, 44% strand | — |
| D | BG505 SOSIPV5.2(7S) - GP120 | protein | 443 | 16% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, H, L, C, D, B, G, E, J, F, K
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains D
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 1035 | 0.83 | 0.84 | 110 | empty |
| 2 | 400 | 0.73 | 0.83 | 53 | NAG |
| 3 | 481 | 0.73 | 0.82 | 54 | NAG |
| 4 | 438 | 0.71 | 0.82 | 67 | NAG |
| 5 | 63 | 0.71 | 0.97 | 25 | empty |
Interfaces
40 interfaces between chains.
- D–F · 2348 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 2314 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2276 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 926 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 913 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 7MEP · BG505 SOSIP.v5.2(7S) in complex with the monoclonal antibodies Rh.33172 mAb.1 and RM19R · 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
- Elsewhere: RCSB PDB 7MEP · PDBe 7MEP
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