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Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 GP120 in C2221 space group
Analyse Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZZ
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- 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, NA, NH2
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 YU2 GP120 glycoprotein | protein | 336 | 18% helix, 38% strand | — |
| R | CD4-mimetic miniprotein M48U1 | protein | 26 | 42% helix, 31% strand | — |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · chains A, R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- NA · Sodium ion · metal · 6 copies · chains A
- NH2 · Amino group · ion · chains A, R
- IPA · Isopropyl alcohol · additive · 5 copies · chains A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.63 | 0.94 | 23 | NA |
| 2 | 178 | 0.61 | 0.83 | 30 | empty |
| 3 | 101 | 0.51 | 0.82 | 22 | NAG, NA |
| 4 | 67 | 0.49 | 0.85 | 22 | empty |
| 5 | 55 | 0.39 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–R · 737 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 8 glycan, 2 covalent, 1 d-amino, 1 modified (disulfide, N-glycosylation, covalent ligand, D-amino acid, nonstandard).
Compared structures
- 4JZZ · 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 4JZZ · PDBe 4JZZ
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