Research workbench
Crystal structure of the D3B subcomplex of the human core snrnp domain at 2.0A resolution
Analyse Crystal structure of the D3B subcomplex of the human core snrnp domain at 2.0A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D3B
- Type
- protein
- Length
- 946 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (small nuclear ribonucleoprotein sm D3); Protein (small nuclear ribonucleoprotein…
- UniProt
- P62318, P14678
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 9 distinct chains · 11% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (small nuclear ribonucleoprotein sm D3) | protein | 72 | 14% helix, 54% strand | P62318 |
| B | Protein (small nuclear ribonucleoprotein associated protein B) | protein | 81 | 7% helix, 57% strand | P14678 |
| C, K | Protein (small nuclear ribonucleoprotein sm D3) | protein | 71 | 14% helix, 55% strand | P62318 |
| D, J | Protein (small nuclear ribonucleoprotein associated protein B) | protein | 86 | 12% helix, 55% strand | P14678 |
| E | Protein (small nuclear ribonucleoprotein sm D3) | protein | 74 | 15% helix, 53% strand | P62318 |
| F | Protein (small nuclear ribonucleoprotein associated protein B) | protein | 83 | 7% helix, 57% strand | P14678 |
| G, I | Protein (small nuclear ribonucleoprotein sm D3) | protein | 73 | 12% helix, 53% strand | P62318 |
| H | Protein (small nuclear ribonucleoprotein associated protein B) | protein | 86 | 8% helix, 55% strand | P14678 |
| L | Protein (small nuclear ribonucleoprotein associated protein B) | protein | 90 | 9% helix, 52% strand | P14678 |
Ligands and binding sites
- GOL · Glycerol · additive · 14 copies · chains A, B, C, D, E, F, J, G, H, I, L
- CIT · Citric acid · additive · 3 copies · chains B, C, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.72 | 0.79 | 50 | GOL |
| 2 | 1120 | 0.70 | 0.75 | 91 | GOL |
| 3 | 616 | 0.70 | 0.79 | 44 | GOL |
| 4 | 66 | 0.47 | 0.84 | 12 | GOL |
| 5 | 71 | 0.46 | 0.83 | 15 | empty |
Interfaces
17 interfaces between chains.
- J–K · 859 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 849 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 824 Ų buried · 11 hydrogen bonds · protein-protein
- H–I · 815 Ų buried · 11 hydrogen bonds · protein-protein
- G–L · 814 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1D3B · Crystal structure of the D3B subcomplex of the human core snrnp domain at 2.0A resolution · 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 P62318
- Every structure of UniProt P14678
- Elsewhere: RCSB PDB 1D3B · PDBe 1D3B · UniProt P62318 · UniProt P14678
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