MolNFT v1 · #142736 · protein
Crystal structure of an enzyme in complex with ligand C
6ADU · Acyclase: “Crystal structure of an enzyme in complex with ligand C”. X-ray diffraction, 3 ligands (9UL, CA, MG), 11 pockets (best druggability 0.85). MolNFT v1 #142736 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ADU
- Type
- protein
- Length
- 795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyclase
- UniProt
- A0A1P8VSI6
- Ligands
- 9UL, CA, MG
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acyclase | protein | 199 | 0% helix, 45% strand | A0A1P8VSI6 |
| D | Acyclase | protein | 198 | 0% helix, 45% strand | A0A1P8VSI6 |
Ligands and binding sites
- 9UL · (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole · ligand · 6 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.85 | 0.91 | 60 | 9UL |
| 2 | 238 | 0.73 | 0.87 | 28 | 9UL |
| 3 | 241 | 0.71 | 0.86 | 27 | 9UL |
| 4 | 122 | 0.66 | 0.89 | 29 | empty |
| 5 | 112 | 0.65 | 0.89 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 877 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 867 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6ADU · Crystal structure of an enzyme in complex with ligand C · 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 A0A1P8VSI6
- Elsewhere: RCSB PDB 6ADU · PDBe 6ADU · UniProt A0A1P8VSI6
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