Research workbench
Crystal structure of compound 10 in complex with HTLV-1 protease
Analyse Crystal structure of compound 10 in complex with HTLV-1 protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YDG
- Type
- protein
- Length
- 219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HTLV-1 protease
- EC
- 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4
- UniProt
- P03362
- Ligands
- G3G, SO4
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HTLV-1 protease (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 108 | 6% helix, 37% strand | P03362 |
| B | HTLV-1 protease (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4) | protein | 111 | 5% helix, 38% strand | P03362 |
Ligands and binding sites
- G3G · N,N'-(3S,4S)-pyrrolidine-3,4-diylbis(4-amino-N-benzylbenzenesulfonamide) · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.63 | 0.75 | 38 | G3G |
Interfaces
1 interface between chains.
- A–B · 1665 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4YDG · Crystal structure of compound 10 in complex with HTLV-1 Protease · 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
- Every structure of UniProt P03362
- Elsewhere: RCSB PDB 4YDG · PDBe 4YDG · UniProt P03362
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