MolNFT v1 · #106370 · protein
Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1 clade a Q842.D12 GP120
4RX4: “Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134 in complex with HIV-1…”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best druggability 0.75). MolNFT v1 #106370 on GenesisL1: 3D…
- PDB
- 4RX4
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade a Q842.D12 GP120; 8ANC134 heavy chain; 8ANC134 light chain
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 clade a Q842.D12 GP120 | protein | 325 | 18% helix, 36% strand | — |
| H | 8ANC134 heavy chain | protein | 217 | 7% helix, 48% strand | — |
| L | 8ANC134 light chain | protein | 212 | 6% helix, 52% strand | — |
| E | HIV-1 clade a Q842.D12 GP120 | protein | 320 | 18% helix, 36% strand | — |
| A | 8ANC134 heavy chain | protein | 222 | 5% helix, 46% strand | — |
| D | 8ANC134 light chain | protein | 213 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains G, L, E, D
- SO4 · Sulfate ion · ion · 12 copies · chains G, H, L, D, E, A
- EDO · 1,2-ethanediol · additive · 5 copies · chains G, H, E
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 | 104 | 0.75 | 0.96 | 27 | empty |
| 2 | 52 | 0.69 | 0.97 | 17 | EDO |
| 3 | 53 | 0.68 | 0.96 | 20 | empty |
| 4 | 78 | 0.63 | 0.90 | 23 | empty |
| 5 | 55 | 0.62 | 0.93 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–D · 1842 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1776 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1131 Ų buried · 16 hydrogen bonds · protein-protein
- E–A · 1083 Ų buried · 16 hydrogen bonds · protein-protein
- G–L · 202 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4RX4 · Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC134… · 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
- Elsewhere: RCSB PDB 4RX4 · PDBe 4RX4
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