MolNFT v1 · #97315 · protein
Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 GP120
4KA2: “Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 GP120”. X-ray diffraction, 3 ligands (MPT, NAG, NH2), 5 pockets (best druggability 0.65). MolNFT v1 #97315 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KA2
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 YU2 GP120; M48U12
- Ligands
- MPT, NAG, NH2
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HIV-1 YU2 GP120 | protein | 337 | 18% helix, 38% strand | — |
| R | M48U12 | protein | 26 | 35% 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
- NH2 · Amino group · ion · chains A, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.65 | 0.94 | 24 | empty |
| 2 | 162 | 0.58 | 0.82 | 28 | empty |
| 3 | 81 | 0.47 | 0.82 | 19 | NAG |
| 4 | 75 | 0.39 | 0.78 | 19 | MPT |
| 5 | 83 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–R · 736 Ų buried · 7 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
- 4KA2 · Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120 · 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 4KA2 · PDBe 4KA2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.