Research workbench
Crystal structure of notf in complex with brevianamide F and dmspp
Analyse Crystal structure of notf in complex with brevianamide F and dmspp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VYA
- Type
- protein
- Length
- 9,288 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxybrevianamide E synthase notf
- EC
- 2.5.1.109
- UniProt
- E0Y3X1
- Ligands
- QRP, DST
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, V, E, G, B, D, F, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, W, X | Deoxybrevianamide E synthase notf (EC 2.5.1.109) | protein | 387 | 40% helix, 19% strand | E0Y3X1 |
Ligands and binding sites
- QRP · (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione · ligand · 24 copies · chains C, A, V, E, G, B, D, F, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, W, X
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 24 copies · chains C, A, V, E, G, B, D, F, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.81 | 0.85 | 81 | QRP, DST |
| 2 | 755 | 0.81 | 0.84 | 83 | QRP, DST |
| 3 | 444 | 0.81 | 0.88 | 52 | QRP, DST |
| 4 | 806 | 0.81 | 0.84 | 88 | QRP, DST |
| 5 | 423 | 0.80 | 0.88 | 45 | QRP, DST |
Interfaces
44 interfaces between chains.
- Q–S · 1179 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1177 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 1174 Ų buried · 16 hydrogen bonds · protein-protein
- J–L · 1159 Ų buried · 15 hydrogen bonds · protein-protein
- M–O · 1130 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 covalent (covalent ligand).
Compared structures
- 6VYA · Crystal structure of NotF in complex with brevianamide F and DMSPP · the same entry in another collection · chain R against R, 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 E0Y3X1
- Elsewhere: RCSB PDB 6VYA · PDBe 6VYA · UniProt E0Y3X1
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