Research workbench
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with HIV-1 env
Analyse Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N28
- Type
- protein
- Length
- 3,523 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; 3BNC117 antibody heavy chain; 3BNC117 antibody light chain…
- UniProt
- I6NF57
- Ligands
- NAG, MAN, BMA, PO4
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 10% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | Envelope glycoprotein GP120 | protein | 472 | 10% helix, 33% strand | I6NF57 |
| C, J, S | 3BNC117 antibody heavy chain | protein | 216 | 1% helix, 39% strand | — |
| D, K, U | 3BNC117 antibody light chain | protein | 204 | 6% helix, 40% strand | — |
| X | J033 antibody heavy chain | protein | 225 | 4% helix, 28% strand | — |
| Y | J033 antibody light chain | protein | 214 | 2% helix, 33% strand | — |
| M, B, N | Envelope glycoprotein GP41 | protein | 136 | 51% helix, 1% strand | I6NF57 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 106 copies · chains A, G, C, D, B, M, F, X, J, K, U, N, S
- MAN · alpha-D-mannopyranose · sugar · 23 copies · chains A, J, D, K, X, C, G, U, F, S
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, D, C, F, K, X, G
- PO4 · Phosphate ion · ion · 3 copies · chains F, G
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 | 896 | 0.80 | 0.82 | 103 | empty |
| 2 | 793 | 0.80 | 0.83 | 88 | empty |
| 3 | 1187 | 0.77 | 0.79 | 65 | empty |
| 4 | 760 | 0.76 | 0.81 | 64 | empty |
| 5 | 97 | 0.73 | 0.95 | 27 | empty |
Interfaces
31 interfaces between chains.
- F–M · 3245 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3157 Ų buried · 20 hydrogen bonds · protein-protein
- G–N · 3127 Ų buried · 19 hydrogen bonds · protein-protein
- X–Y · 2231 Ų buried · 18 hydrogen bonds · protein-protein
- S–U · 1783 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 74 glycan, 52 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7N28 · Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J033 in complex with… · 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 I6NF57
- Elsewhere: RCSB PDB 7N28 · PDBe 7N28 · UniProt I6NF57
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