Research workbench
Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in complex with HIV-1 env
Analyse Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MXD
- Type
- protein
- Length
- 3,519 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 0.79
Structure
electron microscopy · 6 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G | Envelope glycoprotein GP120 | protein | 472 | 10% helix, 39% strand | I6NF57 |
| C, J, S | 3BNC117 antibody heavy chain | protein | 216 | 4% helix, 47% strand | — |
| D, K, U | 3BNC117 antibody light chain | protein | 204 | 5% helix, 34% strand | — |
| X | J038 antibody heavy chain | protein | 221 | 1% helix, 38% strand | — |
| Y | J038 antibody light chain | protein | 214 | 3% helix, 35% strand | — |
| B, I, H | Envelope glycoprotein GP41 | protein | 136 | 47% helix, 7% strand | I6NF57 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 108 copies · chains A, C, D, B, I, F, X, Y, J, K, G, U, H, S
- MAN · alpha-D-mannopyranose · sugar · 27 copies · chains A, J, D, F, S, K, X, G, C, U
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, D, F, K, X, G, U
- PO4 · Phosphate ion · ion · 3 copies · chains A, G, F
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 | 161 | 0.79 | 0.95 | 38 | empty |
| 2 | 938 | 0.78 | 0.80 | 106 | empty |
| 3 | 694 | 0.77 | 0.82 | 78 | empty |
| 4 | 1174 | 0.77 | 0.79 | 63 | empty |
| 5 | 435 | 0.74 | 0.84 | 57 | empty |
Interfaces
31 interfaces between chains.
- A–B · 3157 Ų buried · 22 hydrogen bonds · protein-protein
- F–I · 3141 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 3110 Ų buried · 18 hydrogen bonds · protein-protein
- X–Y · 1992 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1688 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 73 glycan, 53 disulfide (N-glycosylation, disulfide).
Compared structures
- 7MXD · Cryo-EM structure of broadly neutralizing V2-apex-targeting antibody J038 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 7MXD · PDBe 7MXD · UniProt I6NF57
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