Research workbench
Crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 GP120 envelope glycoprotein and anti-HIV-1 antibody 17B
Analyse Crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYM
- Type
- protein
- Length
- 1,538 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exterior membrane GLYCOPROTEIN(GP120),EXTERIOR membrane GLYCOPROTEIN(GP120),EXTERIOR…
- UniProt
- P35961
- Ligands
- MPT, NAG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Exterior membrane GLYCOPROTEIN(GP120),EXTERIOR membrane GLYCOPROTEIN(GP120),EXTERIOR membrane GLYCOPROTEIN(GP120) | protein | 301 | 18% helix, 39% strand | P35961 |
| L, Q | Antibody 17B light chain | protein | 214 | 6% helix, 50% strand | — |
| H, R | Antibody 17B heavy chain | protein | 229 | 9% helix, 50% strand | — |
| M, S | F23, scorpion-toxin mimic of CD4 | protein | 26 | 35% helix, 31% strand | — |
| P | Exterior membrane GLYCOPROTEIN(GP120),EXTERIOR membrane GLYCOPROTEIN(GP120),EXTERIOR membrane GLYCOPROTEIN(GP120) | protein | 299 | 18% helix, 38% strand | P35961 |
Ligands and binding sites
- MPT · Beta-mercaptopropionic acid · ligand · 2 copies · chains G, M, P, S
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains G, P
- EDO · 1,2-ethanediol · additive · 2 copies · chains G, M
- IPA · Isopropyl alcohol · additive · 2 copies · chains G, M, P, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.68 | 0.82 | 36 | NAG |
| 2 | 308 | 0.65 | 0.81 | 30 | NAG |
| 3 | 208 | 0.62 | 0.83 | 31 | empty |
| 4 | 502 | 0.62 | 0.75 | 61 | empty |
| 5 | 455 | 0.61 | 0.75 | 51 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1926 Ų buried · 18 hydrogen bonds · protein-protein
- Q–R · 1859 Ų buried · 13 hydrogen bonds · protein-protein
- H–R · 769 Ų buried · 11 hydrogen bonds · protein-protein
- P–S · 546 Ų buried · 6 hydrogen bonds · protein-protein
- P–R · 531 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 16 glycan, 4 covalent, 2 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 1YYM · crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120… · 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
- Every structure of UniProt P35961
- Elsewhere: RCSB PDB 1YYM · PDBe 1YYM · UniProt P35961
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