Research workbench
BG505 sosip MD39 in complex with the monoclonal antibodies RH.33104 MAB.1 and RM20A3
Analyse BG505 sosip MD39 in complex with the monoclonal antibodies RH.33104 MAB.1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MDU
- Type
- protein
- Length
- 1,018 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RH.33104 MAB.1 heavy chain; Surface protein GP120; RM20A3 mab heavy chain; RM20A3 mab…
- UniProt
- Q2N0S6
- Ligands
- NAG, MAN, BMA
- Pockets
- 15 · best druggability 0.67
Structure
electron microscopy · 6 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | RH.33104 MAB.1 heavy chain | protein | 114 | 5% helix, 48% strand | — |
| A | Surface protein GP120 | protein | 445 | 11% helix, 44% strand | Q2N0S6 |
| E | RM20A3 mab heavy chain | protein | 123 | 10% helix, 50% strand | — |
| F | RM20A3 mab light chain | protein | 108 | 0% helix, 42% strand | — |
| L | RH.33104 MAB.1 light chain | protein | 105 | 3% helix, 50% strand | — |
| B | Transmembrane protein GP41 | protein | 123 | 60% helix, 6% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, L, E
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.67 | 0.95 | 20 | empty |
| 2 | 292 | 0.66 | 0.82 | 54 | NAG |
| 3 | 409 | 0.64 | 0.78 | 43 | empty |
| 4 | 263 | 0.60 | 0.80 | 31 | empty |
| 5 | 96 | 0.51 | 0.82 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2395 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 863 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 796 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 589 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 562 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 7MDU · BG505 SOSIP MD39 in complex with the monoclonal antibodies Rh.33104 mAb.1 and RM20A3 · the same entry in another collection · chain H against H, 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 7MDU · PDBe 7MDU · UniProt Q2N0S6
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