MolNFT v1 · #110998 · protein
Crystal structure of broadly and potently neutralizing antibody C38- VRC16.01 in complex with HIV-1 clade ae strain 93TH057 GP120
4YDK · Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160: “Crystal structure of broadly and potently neutralizing antibody C38- VRC16.01 in complex with HIV-1 clade ae…”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best…
- PDB
- 4YDK
- Type
- protein
- Length
- 785 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160; Heavy chain of antibody…
- UniProt
- Q0ED31
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 341 | 18% helix, 37% strand | Q0ED31 |
| H | Heavy chain of antibody C38-VRC16.01 | protein | 230 | 7% helix, 51% strand | — |
| L | Light chain of antibody C38-VRC16.01 | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G
- GOL · Glycerol · additive · 13 copies · chains G, H, L
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains G, L, H
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.58 | 0.79 | 34 | empty |
| 2 | 355 | 0.56 | 0.75 | 38 | PEG |
| 3 | 246 | 0.53 | 0.76 | 29 | GOL |
| 4 | 69 | 0.53 | 0.86 | 18 | NAG |
| 5 | 200 | 0.45 | 0.74 | 38 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2024 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 963 Ų buried · 23 hydrogen bonds · protein-protein
- G–L · 346 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4YDK · Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex… · 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 4YDK · PDBe 4YDK · UniProt Q0ED31
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