MolNFT v1 · #68961 · protein
Crystal structure of the gld-1 homodimerization domain from caenorhabditis elegans N169A mutant at 2.28 a resolution
3KBL · Female germline-specific tumor suppressor gld-1: “Crystal structure of the gld-1 homodimerization domain from caenorhabditis elegans N169A mutant at 2.28 a…”. X-ray diffraction, 3 pockets (best druggability 0.36). MolNFT v1 #68961…
- PDB
- 3KBL
- Type
- protein
- Length
- 200 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Female germline-specific tumor suppressor gld-1
- UniProt
- Q17339
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Female germline-specific tumor suppressor gld-1 | protein | 54 | 67% helix, 0% strand | Q17339 |
| B, D | Female germline-specific tumor suppressor gld-1 | protein | 46 | 70% helix, 0% strand | Q17339 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.36 | 0.76 | 17 | empty |
| 2 | 74 | 0.36 | 0.77 | 18 | empty |
| 3 | 64 | 0.29 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 794 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 741 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 213 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3KBL · Crystal structure of the GLD-1 homodimerization domain from Caenorhabditis elegans N169A… · the same entry in another collection · chain D against D, TM-score 1.00
- Q17339 · AlphaFold monomer V2.0 prediction for female germline-specific tumor suppressor gld-1… · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q17339
- Elsewhere: RCSB PDB 3KBL · PDBe 3KBL · UniProt Q17339
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