Research workbench
Crystal structure of rhodesain in complex with a macrolactam inhibitor
Analyse Crystal structure of rhodesain in complex with a macrolactam inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EXO
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine protease
- UniProt
- Q95PM0
- Ligands
- C3E
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cysteine protease | protein | 215 | 27% helix, 23% strand | Q95PM0 |
Ligands and binding sites
- C3E · (3~{S},14~{E})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.78 | 0.86 | 47 | EDO |
| 2 | 72 | 0.32 | 0.75 | 18 | EDO |
| 3 | 64 | 0.32 | 0.76 | 17 | C3E |
| 4 | 74 | 0.32 | 0.74 | 18 | empty |
| 5 | 73 | 0.31 | 0.74 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 506 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 6EXO · Crystal Structure of Rhodesain in complex with a Macrolactam Inhibitor · 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 Q95PM0
- Elsewhere: RCSB PDB 6EXO · PDBe 6EXO · UniProt Q95PM0
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