MolNFT v1 · #139570 · protein
Crystal structure of the GEMIN2-binding domain of smn, GEMIN2 in complex with SMD1(1-82)/D2.R61A/F/E/G from human
5XJT · Gem-associated protein 2: “Crystal structure of the GEMIN2-binding domain of smn, GEMIN2 in complex with SMD1(1-82)/D2.R61A/F/E/G from…”. X-ray diffraction, 11 pockets (best druggability 0.57). MolNFT v1 #139570 on GenesisL1: 3D…
- PDB
- 5XJT
- Type
- protein
- Length
- 617 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gem-associated protein 2; Small nuclear ribonucleoprotein sm D1; Small nuclear…
- UniProt
- O14893, P62314, P62316, P62304, P62306, P62308, Q16637
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | Gem-associated protein 2 | protein | 217 | 54% helix, 1% strand | O14893 |
| A | Small nuclear ribonucleoprotein sm D1 | protein | 80 | 14% helix, 46% strand | P62314 |
| B | Small nuclear ribonucleoprotein sm D2 | protein | 91 | 23% helix, 51% strand | P62316 |
| E | Small nuclear ribonucleoprotein E | protein | 75 | 19% helix, 55% strand | P62304 |
| F | Small nuclear ribonucleoprotein F | protein | 74 | 12% helix, 57% strand | P62306 |
| G | Small nuclear ribonucleoprotein G | protein | 63 | 0% helix, 57% strand | P62308 |
| M | Survival motor neuron protein | protein | 17 | 65% helix, 0% strand | Q16637 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.57 | 0.77 | 50 | empty |
| 2 | 204 | 0.56 | 0.79 | 27 | empty |
| 3 | 208 | 0.49 | 0.76 | 26 | empty |
| 4 | 167 | 0.49 | 0.77 | 31 | empty |
| 5 | 93 | 0.45 | 0.80 | 18 | empty |
Interfaces
11 interfaces between chains.
- 2–B · 1083 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 968 Ų buried · 17 hydrogen bonds · protein-protein
- 2–F · 886 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 885 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 874 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5XJT · Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with… · the same entry in another collection · chain M against M, TM-score 1.00
- O14893 · AlphaFold monomer V2.0 prediction for gem-associated protein 2 (O14893) · a predicted model of the same protein · chain 2 against A, TM-score 0.95
- Q16637 · AlphaFold monomer V2.0 prediction for survival motor neuron protein (Q16637) · a predicted model of the same protein · chain M against A, TM-score 0.66
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 O14893
- Every structure of UniProt P62314
- Every structure of UniProt P62316
- Every structure of UniProt P62304
- Every structure of UniProt P62306
- Every structure of UniProt P62308
- Every structure of UniProt Q16637
- Elsewhere: RCSB PDB 5XJT · PDBe 5XJT · UniProt O14893 · UniProt P62314 · UniProt P62316 · UniProt P62304 · UniProt P62306 · UniProt P62308 · UniProt Q16637
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