Research workbench
Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis
Analyse Conversion of a disulfide bond into a thioacetal group during echinomycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NEC
- Type
- protein
- Length
- 986 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative SAM-dependent methyltransferase; Echinomycin
- UniProt
- Q0X0A7
- Ligands
- QUI, SAH, NA
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative SAM-dependent methyltransferase | protein | 238 | 37% helix, 25% strand | Q0X0A7 |
| E, F, G, H | Echinomycin | protein | 8 | 0% helix, 0% strand | — |
| B | Putative SAM-dependent methyltransferase | protein | 244 | 37% helix, 24% strand | Q0X0A7 |
| C | Putative SAM-dependent methyltransferase | protein | 233 | 36% helix, 26% strand | Q0X0A7 |
| D | Putative SAM-dependent methyltransferase | protein | 239 | 38% helix, 26% strand | Q0X0A7 |
Ligands and binding sites
- QUI · 2-carboxyquinoxaline · ligand · 8 copies · chains A, E, B, F, C, G, D, H
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- NA · Sodium ion · metal · 3 copies · chains A, D, C
- PGE · Triethylene glycol · additive · 2 copies · chains A, C, D
- 15P · Polyethylene glycol (N=34) · additive · 2 copies · chains D, H, A
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.81 | 0.95 | 43 | SAH |
| 2 | 266 | 0.81 | 0.93 | 49 | SAH |
| 3 | 252 | 0.81 | 0.93 | 55 | SAH |
| 4 | 218 | 0.80 | 0.93 | 44 | SAH |
| 5 | 901 | 0.73 | 0.78 | 68 | empty |
Interfaces
8 interfaces between chains.
- B–C · 993 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 943 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 553 Ų buried · 1 hydrogen bond · protein-protein
- D–H · 547 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 542 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 8 covalent, 8 d-amino (covalent ligand, D-amino acid, methylation, nonstandard).
Compared structures
- 4NEC · Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis · 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 Q0X0A7
- Elsewhere: RCSB PDB 4NEC · PDBe 4NEC · UniProt Q0X0A7
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