MolNFT v1 · #147238 · protein
Dieckmann cyclase, ncmc, bound to cerulenin
6E6T: “Dieckmann cyclase, ncmc, bound to cerulenin”. X-ray diffraction, 2 ligands (HVV, SO4), 8 pockets (best druggability 0.71). MolNFT v1 #147238 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6E6T
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ncmc
- UniProt
- A0A1X9WEN9
- Ligands
- HVV, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ncmc | protein | 266 | 53% helix, 13% strand | A0A1X9WEN9 |
| B | Ncmc | protein | 259 | 52% helix, 13% strand | A0A1X9WEN9 |
Ligands and binding sites
- HVV · (4S,5R)-4,5-dihydroxy-5-[(3E,6E)-octa-3,6-dien-1-yl]pyrrolidin-2-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.71 | 0.76 | 75 | HVV |
| 2 | 348 | 0.69 | 0.82 | 36 | HVV |
| 3 | 83 | 0.51 | 0.83 | 18 | empty |
| 4 | 98 | 0.38 | 0.76 | 17 | empty |
| 5 | 88 | 0.33 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 160 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6E6T · Dieckmann cyclase, NcmC, bound to cerulenin · 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 A0A1X9WEN9
- Elsewhere: RCSB PDB 6E6T · PDBe 6E6T · UniProt A0A1X9WEN9
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