MolNFT v1 · #182005 · protein
BG505 sosip MD39 in complex with the monoclonal antibodies RH.33104 MAB.1 and RM20A3
7MDU · RH.33104 MAB.1 heavy chain: “BG505 sosip MD39 in complex with the monoclonal antibodies RH.33104 MAB.1 and RM20A3”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 15 pockets (best druggability 0.67). MolNFT v1 #182005 on GenesisL1…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.