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Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 GP120
Analyse Crystal structure of broadly and potently neutralizing antibody VRC01 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NGB
- Type
- protein
- Length
- 3,127 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160; Antigen binding fragment of heavy chain: antibody VRC01…
- UniProt
- Q0ED31
- Ligands
- NAG, BGC, MAN, BMA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 13% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160 | protein | 347 | 18% helix, 34% strand | Q0ED31 |
| H, B, E, J | Antigen binding fragment of heavy chain: antibody VRC01 | protein | 224 | 6% helix, 49% strand | — |
| L, F | Antigen binding fragment of light chain: antibody VRC01 | protein | 208 | 5% helix, 50% strand | — |
| A | Envelope glycoprotein GP160 | protein | 349 | 15% helix, 34% strand | Q0ED31 |
| C, K | Antigen binding fragment of light chain: antibody VRC01 | protein | 210 | 5% helix, 47% strand | — |
| D | Envelope glycoprotein GP160 | protein | 350 | 16% helix, 36% strand | Q0ED31 |
| I | Envelope glycoprotein GP160 | protein | 349 | 15% helix, 35% strand | Q0ED31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 54 copies · chains L, C, F, K, G, A, E, D, I
- BGC · beta-D-glucopyranose · sugar · 13 copies · chains G, E, A, B, J, C, H, D, I
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 3 copies
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 7 copies · chains A, D, I, B, J, K
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 | 1148 | 0.82 | 0.83 | 118 | BGC, TRS |
| 2 | 634 | 0.80 | 0.85 | 64 | TRS, BGC |
| 3 | 300 | 0.75 | 0.87 | 38 | empty |
| 4 | 427 | 0.75 | 0.84 | 68 | BGC |
| 5 | 704 | 0.73 | 0.79 | 69 | empty |
Interfaces
21 interfaces between chains.
- J–K · 2055 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1933 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1931 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 1804 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 978 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide, 50 glycan (disulfide, N-glycosylation).
Compared structures
- 3NGB · Crystal structure of broadly and potently neutralizing antibody VRC01 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 3NGB · PDBe 3NGB · UniProt Q0ED31
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