MolNFT v2 · #221299 · protein
Cryo-EM structure of HmAb64 scFv in complex with CNE40 SOSIP trimer
8TR3 · CNE40 SOSIP Envelope glycoprotein gp120: “Cryo-EM structure of HmAb64 scFv in complex with CNE40 SOSIP trimer”. Electron microscopy at 3.74, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v2 #221299 on GenesisL1: 3D…
- PDB
- 8TR3
- Type
- protein
- Length
- 2,028 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.74
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- CNE40 SOSIP Envelope glycoprotein gp120; CNE40 SOSIP Transmembrane protein gp41; HmAb64…
- UniProt
- D7S2E5
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.74 · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | CNE40 SOSIP Envelope glycoprotein gp120 | protein | 312 | 13% helix, 34% strand | D7S2E5 |
| B, D, F | CNE40 SOSIP Transmembrane protein gp41 | protein | 132 | 65% helix, 2% strand | D7S2E5 |
| H, I, J | HmAb64 Fv heavy chain | protein | 124 | 5% helix, 49% strand | — |
| L, M, N | HmAb64 Fv light chain | protein | 108 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, C, E, B, D, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.87 | 0.94 | 74 | empty |
| 2 | 1103 | 0.76 | 0.78 | 106 | empty |
| 3 | 1037 | 0.76 | 0.78 | 94 | empty |
| 4 | 994 | 0.76 | 0.78 | 90 | empty |
| 5 | 405 | 0.75 | 0.85 | 84 | NAG |
Interfaces
21 interfaces between chains.
- C–D · 2208 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 2207 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1092 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 1091 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 30 disulfide (N-glycosylation, disulfide).
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 D7S2E5
- Elsewhere: RCSB PDB 8TR3 · PDBe 8TR3 · UniProt D7S2E5
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