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The structure of dcsb complex with its substrate analogue
Analyse The structure of dcsb complex with its substrate analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D79
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dltd domain-containing protein
- UniProt
- J4WAT9
- Ligands
- GY0, GYF, NA, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Dltd domain-containing protein | protein | 295 | 35% helix, 20% strand | J4WAT9 |
| A | Dltd domain-containing protein | protein | 293 | 35% helix, 20% strand | J4WAT9 |
| B | Dltd domain-containing protein | protein | 290 | 36% helix, 20% strand | J4WAT9 |
| C | Dltd domain-containing protein | protein | 290 | 35% helix, 20% strand | J4WAT9 |
Ligands and binding sites
- GY0 · methyl 3-[(E,3R,9R)-3,9-bis(oxidanyl)dec-4-enoyl]sulfanylpropanoate · ligand · chains D
- GYF · methyl 3-sulfanylpropanoate · ligand · chains B
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 4 copies · chains D, A, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains D, B, A
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.77 | 0.79 | 91 | EDO |
| 2 | 87 | 0.75 | 0.96 | 22 | GOL |
| 3 | 125 | 0.74 | 0.92 | 25 | GOL |
| 4 | 129 | 0.73 | 0.92 | 29 | GY0 |
| 5 | 526 | 0.71 | 0.80 | 43 | empty |
Interfaces
5 interfaces between chains.
- D–A · 1820 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 314 Ų buried · 1 hydrogen bond · protein-protein
- D–C · 275 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 269 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 86 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7D79 · The structure of DcsB complex with its substrate analogue · the same entry in another collection · chain D against D, 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 J4WAT9
- Elsewhere: RCSB PDB 7D79 · PDBe 7D79 · UniProt J4WAT9
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