MolNFT v1 · #96650 · protein
Crystal structure of broadly and potently neutralizing antibody 12A21 in complex with HIV-1 strain 93TH057 GP120 mutant
4JPW · HIV-1 clade A/E strain 73TH057 GP120 with mutation H375S: “Crystal structure of broadly and potently neutralizing antibody 12A21 in complex with HIV-1 strain 93TH057…”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best…
- PDB
- 4JPW
- Type
- protein
- Length
- 776 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 clade A/E strain 73TH057 GP120 with mutation H375S; Heavy chain of antibody 12A21…
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | HIV-1 clade A/E strain 73TH057 GP120 with mutation H375S | protein | 345 | 17% helix, 37% strand | — |
| H | Heavy chain of antibody 12A21 | protein | 223 | 8% helix, 51% strand | — |
| L | Light chain of antibody 12A21 | protein | 208 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.75 | 0.88 | 50 | empty |
| 2 | 90 | 0.65 | 0.90 | 25 | empty |
| 3 | 493 | 0.62 | 0.75 | 58 | empty |
| 4 | 58 | 0.52 | 0.87 | 18 | NAG |
| 5 | 164 | 0.46 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1760 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1135 Ų buried · 16 hydrogen bonds · protein-protein
- G–L · 228 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4JPW · Crystal structure of broadly and potently neutralizing antibody 12a21 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
- Elsewhere: RCSB PDB 4JPW · PDBe 4JPW
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