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Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex with HIV-1 clade ae strain 93TH057 GP120 core
Analyse Crystal structure of broadly neutralizing VRC01-class antibody N6 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TE6
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clade A/E 93TH057 HIV-1 GP120 core; Heavy chain of N6; Light chain of N6
- UniProt
- A0A0M3KKW9
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Clade A/E 93TH057 HIV-1 GP120 core | protein | 341 | 19% helix, 37% strand | A0A0M3KKW9 |
| H | Heavy chain of N6 | protein | 223 | 7% helix, 48% strand | — |
| L | Light chain of N6 | protein | 210 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.75 | 0.87 | 49 | empty |
| 2 | 67 | 0.57 | 0.88 | 16 | NAG |
| 3 | 317 | 0.52 | 0.74 | 36 | empty |
| 4 | 189 | 0.49 | 0.76 | 29 | empty |
| 5 | 136 | 0.46 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1784 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 939 Ų buried · 25 hydrogen bonds · protein-protein
- G–L · 222 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 5TE6 · Crystal Structure of Broadly Neutralizing VRC01-class Antibody N6 in Complex with HIV-1… · the same entry in another collection · chain G against G, 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 A0A0M3KKW9
- Elsewhere: RCSB PDB 5TE6 · PDBe 5TE6 · UniProt A0A0M3KKW9
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