Research workbench
Structure of human dcps bound to M7GDP
Analyse Structure of human dcps bound to M7GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XMM
- Type
- protein
- Length
- 1,156 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock-like protein 1
- Ligands
- G7M, M7G, PO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Heat shock-like protein 1 | protein | 288 | 33% helix, 29% strand | — |
| A | Heat shock-like protein 1 | protein | 287 | 33% helix, 29% strand | — |
| C | Heat shock-like protein 1 | protein | 289 | 33% helix, 29% strand | — |
| D | Heat shock-like protein 1 | protein | 292 | 32% helix, 29% strand | — |
Ligands and binding sites
- G7M · N7-methyl-guanosine-5'-monophosphate · ligand · 2 copies · chains B, C
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · 2 copies · chains B, A, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.86 | 0.87 | 89 | PO4, M7G |
| 2 | 1186 | 0.86 | 0.87 | 121 | PO4, M7G |
| 3 | 176 | 0.78 | 0.94 | 30 | empty |
| 4 | 162 | 0.75 | 0.92 | 29 | empty |
| 5 | 476 | 0.69 | 0.79 | 38 | empty |
Interfaces
4 interfaces between chains.
- C–D · 4890 Ų buried · 80 hydrogen bonds · protein-protein
- B–A · 4875 Ų buried · 77 hydrogen bonds · protein-protein
- B–D · 688 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1XMM · Structure of human Dcps bound to m7GDP · 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
- Elsewhere: RCSB PDB 1XMM · PDBe 1XMM
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