Research workbench
Shrimp dutpase in complex with stl
Analyse Shrimp dutpase in complex with stl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DLV
- Type
- protein
- Length
- 1,664 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shrimp dutpase; ORF20
- UniProt
- Q9F0J8
- Ligands
- CA, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shrimp dutpase | protein | 131 | 5% helix, 46% strand | — |
| B | Shrimp dutpase | protein | 137 | 5% helix, 45% strand | — |
| C, G, I | Shrimp dutpase | protein | 136 | 5% helix, 44% strand | — |
| D, K | ORF20 | protein | 144 | 72% helix, 0% strand | Q9F0J8 |
| E | ORF20 | protein | 141 | 73% helix, 0% strand | Q9F0J8 |
| F, L | ORF20 | protein | 143 | 72% helix, 0% strand | Q9F0J8 |
| H | Shrimp dutpase | protein | 127 | 6% helix, 48% strand | — |
| J | ORF20 | protein | 146 | 70% helix, 0% strand | Q9F0J8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C, G, H, I
- SO4 · Sulfate ion · ion · 9 copies · chains A, D, B, C, F, G, H, I, K, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.97 | 26 | CA |
| 2 | 117 | 0.78 | 0.98 | 29 | CA |
| 3 | 530 | 0.75 | 0.83 | 72 | SO4 |
| 4 | 814 | 0.75 | 0.79 | 98 | empty |
| 5 | 78 | 0.75 | 0.98 | 27 | empty |
Interfaces
30 interfaces between chains.
- A–C · 1903 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1861 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1852 Ų buried · 21 hydrogen bonds · protein-protein
- G–I · 1832 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1789 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7DLV · shrimp dUTPase in complex with Stl · the same entry in another collection · chain B against B, 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 Q9F0J8
- Elsewhere: RCSB PDB 7DLV · PDBe 7DLV · UniProt Q9F0J8
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