MolNFT v1 · #157448 · protein
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 fabs bound, sharpened MAP
6MZJ · 426C ds-sosip D3: “Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 fabs bound, sharpened MAP”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #157448…
- PDB
- 6MZJ
- Type
- protein
- Length
- 2,088 residues
- Chains
- 7
- 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 0.85
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 | VRC01GL light chain | protein | 100 | 3% helix, 44% strand | Q6PJF2 |
| H, D | 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, B, D, E
- MAN · alpha-D-mannopyranose · sugar · 32 copies · chains A, H, B, D, E
- BMA · beta-D-mannopyranose · sugar · 21 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 | 1052 | 0.85 | 0.87 | 139 | empty |
| 2 | 925 | 0.85 | 0.87 | 138 | empty |
| 3 | 696 | 0.82 | 0.86 | 101 | empty |
| 4 | 810 | 0.80 | 0.84 | 133 | empty |
| 5 | 638 | 0.79 | 0.84 | 92 | empty |
Interfaces
9 interfaces between chains.
- A–B · 444 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 437 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 435 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 304 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 304 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 42 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).
Compared structures
- 6MZJ · Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 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 6MZJ · PDBe 6MZJ · UniProt Q6PJF2 · UniProt S6C4S0
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