MolNFT v1 · #110999 · protein
Crystal structure of broadly and potently neutralizing antibody C38- VRC18.02 in complex with HIV-1 clade ae strain 93TH057GP120
4YDL · Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160: “Crystal structure of broadly and potently neutralizing antibody C38- VRC18.02 in complex with HIV-1 clade ae…”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best…
- PDB
- 4YDL
- Type
- protein
- Length
- 1,557 residues
- Chains
- 6
- 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, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 344 | 18% helix, 37% strand | Q0ED31 |
| H, B | Heavy chain of antibody C38-VRC18.02 | protein | 224 | 8% helix, 52% strand | — |
| L, C | Light chain of antibody C38-VRC18.02 | protein | 211 | 8% helix, 51% strand | — |
| A | Envelope glycoprotein GP160,ENVELOPE glycoprotein GP160 | protein | 343 | 18% helix, 36% strand | Q0ED31 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains G, L, A, C
- SO4 · Sulfate ion · ion · 3 copies · chains L, C, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.82 | 0.83 | 126 | empty |
| 2 | 212 | 0.70 | 0.87 | 40 | empty |
| 3 | 69 | 0.68 | 0.95 | 26 | empty |
| 4 | 283 | 0.67 | 0.83 | 31 | EPE |
| 5 | 441 | 0.66 | 0.79 | 35 | empty |
Interfaces
8 interfaces between chains.
- H–L · 1847 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1811 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 964 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 20 hydrogen bonds · protein-protein
- G–A · 432 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 22 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4YDL · Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 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 4YDL · PDBe 4YDL · UniProt Q0ED31
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