MolNFT v1 · #110150 · protein
Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain 93TH057 GP120
4XNZ · Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160: “Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with HIV-1 clade A/E strain…”. X-ray diffraction, 2 ligands (NAG, FUC), 20 pockets (best…
- PDB
- 4XNZ
- Type
- protein
- Length
- 2,294 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160; Heavy chain of antibody VRC06B…
- UniProt
- Q0ED31
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 340 | 15% helix, 36% strand | Q0ED31 |
| H | Heavy chain of antibody VRC06B | protein | 222 | 3% helix, 48% strand | — |
| L | Light chain of antibody VRC06B | protein | 207 | 4% helix, 41% strand | — |
| A | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 341 | 16% helix, 35% strand | Q0ED31 |
| B | Heavy chain of antibody VRC06B | protein | 222 | 1% helix, 49% strand | — |
| C | Light chain of antibody VRC06B | protein | 206 | 2% helix, 39% strand | — |
| D | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 330 | 14% helix, 35% strand | Q0ED31 |
| E | Heavy chain of antibody VRC06B | protein | 220 | 8% helix, 47% strand | — |
| F | Light chain of antibody VRC06B | protein | 206 | 4% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains L, C, F, G, A, D
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains L, C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.71 | 0.82 | 48 | empty |
| 2 | 537 | 0.70 | 0.79 | 56 | empty |
| 3 | 443 | 0.69 | 0.80 | 48 | empty |
| 4 | 147 | 0.67 | 0.88 | 27 | empty |
| 5 | 581 | 0.62 | 0.74 | 64 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1843 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 1795 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1692 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1104 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1042 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 4XNZ · Crystal structure of broadly and potently neutralizing antibody VRC06B in complex with… · 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 Q0ED31
- Elsewhere: RCSB PDB 4XNZ · PDBe 4XNZ · UniProt Q0ED31
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