Research workbench
Cryo-EM model of HIV-1 env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11A fragment antigen binding variable domain
Analyse Cryo-EM model of HIV-1 env BG505 SOSIP.664 in complex with rabbit monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X97
- Type
- protein
- Length
- 2,319 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 HIV-1 env GP120; BG505 HIV-1 env GP41; Monoclonal antibody 11A fragment antigen…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | BG505 HIV-1 env GP120 | protein | 427 | 13% helix, 45% strand | Q2N0S6 |
| B, D, I | BG505 HIV-1 env GP41 | protein | 117 | 62% helix, 8% strand | Q2N0S6 |
| H, E, J | Monoclonal antibody 11A fragment antigen binding heavy chain | protein | 118 | 5% helix, 56% strand | — |
| L, F, K | Monoclonal antibody 11A kappa chain | protein | 111 | 0% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, B, L, C, D, F, G, I, K
- 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.81 | 0.87 | 65 | empty |
| 2 | 59 | 0.71 | 0.98 | 25 | empty |
| 3 | 50 | 0.68 | 0.97 | 25 | empty |
| 4 | 50 | 0.68 | 0.97 | 25 | empty |
| 5 | 70 | 0.66 | 0.93 | 26 | empty |
Interfaces
21 interfaces between chains.
- C–D · 2694 Ų buried · 29 hydrogen bonds · protein-protein
- G–I · 2694 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2689 Ų buried · 29 hydrogen bonds · protein-protein
- D–I · 998 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 998 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 42 glycan (disulfide, N-glycosylation).
Compared structures
- 6X97 · Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11A… · 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 Q2N0S6
- Elsewhere: RCSB PDB 6X97 · PDBe 6X97 · UniProt Q2N0S6
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