MolNFT v1 · #96981 · protein
Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 GP120 in P212121 space group
4JZW · HIV-1 YU2 GP120 glycoprotein: “Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 GP120 in P212121 space group”. X-ray diffraction, 4 ligands (MPT, NAG, NH2), 12 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 4JZW
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 YU2 GP120 glycoprotein; CD4-mimetic miniprotein M48U1
- Ligands
- MPT, NAG, NH2, SO4
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 YU2 GP120 glycoprotein | protein | 336 | 17% helix, 39% strand | — |
| G | HIV-1 YU2 GP120 glycoprotein | protein | 339 | 18% helix, 38% strand | — |
| M, R | CD4-mimetic miniprotein M48U1 | protein | 26 | 38% helix, 31% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains G, M, A, R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, G
- NH2 · Amino group · ion · 2 copies · chains G, M, A, R
- SO4 · Sulfate ion · ion · 2 copies · chains A, G
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, M, R, G
- EDO · 1,2-ethanediol · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.61 | 0.82 | 30 | empty |
| 2 | 218 | 0.60 | 0.81 | 33 | empty |
| 3 | 70 | 0.51 | 0.85 | 22 | empty |
| 4 | 70 | 0.50 | 0.85 | 22 | empty |
| 5 | 63 | 0.48 | 0.84 | 21 | NAG |
Interfaces
4 interfaces between chains.
- A–R · 746 Ų buried · 7 hydrogen bonds · protein-protein
- G–M · 739 Ų buried · 7 hydrogen bonds · protein-protein
- A–G · 179 Ų buried · 5 hydrogen bonds · protein-protein
- G–R · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 17 disulfide, 4 covalent, 2 d-amino, 2 modified (N-glycosylation, disulfide, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 4JZW · Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in… · the same entry in another collection · chain A against A, 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 4JZW · PDBe 4JZW
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