MolNFT v1 · #157434 · protein
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 fabs bound, sharpened MAP
6MYY · 426C ds-sosip D3: “Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 fabs bound, sharpened MAP”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #157434…
- PDB
- 6MYY
- Type
- protein
- Length
- 2,307 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 426C ds-sosip D3; VRC01GL light chain; VRC01GL heavy chain
- UniProt
- Q6PJF2, S6C4S0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | 426C ds-sosip D3 | protein | 550 | 25% helix, 33% strand | — |
| L, C, F | VRC01GL light chain | protein | 100 | 3% helix, 44% strand | Q6PJF2 |
| H, D, G | VRC01GL heavy chain | protein | 119 | 10% helix, 48% strand | S6C4S0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 96 copies · chains A, H, E, B, D, G
- MAN · alpha-D-mannopyranose · sugar · 36 copies · chains A, H, B, D, E, G
- BMA · beta-D-mannopyranose · sugar · 24 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 | 474 | 0.83 | 0.90 | 56 | empty |
| 2 | 421 | 0.73 | 0.83 | 49 | empty |
| 3 | 468 | 0.72 | 0.82 | 52 | empty |
| 4 | 442 | 0.72 | 0.82 | 44 | empty |
| 5 | 75 | 0.70 | 0.95 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1348 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 1343 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 821 Ų buried · 15 hydrogen bonds · protein-protein
- E–G · 820 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 45 disulfide, 3 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 6MYY · Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs… · the same entry in another collection · chain A against A, 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 Q6PJF2
- Every structure of UniProt S6C4S0
- Elsewhere: RCSB PDB 6MYY · PDBe 6MYY · UniProt Q6PJF2 · UniProt S6C4S0
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