Research workbench
Structure of gld-2/RNP-8 complex
Analyse Structure of gld-2/RNP-8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JNB
- Type
- protein
- Length
- 1,350 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(A) RNA polymerase gld-2; Rnp (rrm RNA binding domain) containing
- EC
- 2.7.7.19
- UniProt
- O17087, O61711
- Ligands
- MG, SO4
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(A) RNA polymerase gld-2 (EC 2.7.7.19) | protein | 329 | 43% helix, 15% strand | O17087 |
| B | POLY(A) RNA polymerase gld-2 (EC 2.7.7.19) | protein | 324 | 44% helix, 15% strand | O17087 |
| C | POLY(A) RNA polymerase gld-2 (EC 2.7.7.19) | protein | 289 | 46% helix, 15% strand | O17087 |
| D | POLY(A) RNA polymerase gld-2 (EC 2.7.7.19) | protein | 263 | 43% helix, 15% strand | O17087 |
| E, F | Rnp (rrm RNA binding domain) containing | protein | 46 | 33% helix, 7% strand | O61711 |
| G | Rnp (rrm RNA binding domain) containing | protein | 28 | 46% helix, 0% strand | O61711 |
| H | Rnp (rrm RNA binding domain) containing | protein | 25 | 60% helix, 0% strand | O61711 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, F, B, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, F, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.82 | 0.83 | 117 | EDO |
| 2 | 401 | 0.74 | 0.85 | 65 | SO4, MG, EDO |
| 3 | 426 | 0.73 | 0.84 | 69 | SO4, EDO, MG |
| 4 | 463 | 0.63 | 0.76 | 41 | SO4, EDO |
| 5 | 179 | 0.58 | 0.81 | 32 | EDO |
Interfaces
15 interfaces between chains.
- A–E · 1767 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1766 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 1249 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 1248 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 954 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 O17087
- Every structure of UniProt O61711
- Elsewhere: RCSB PDB 5JNB · PDBe 5JNB · UniProt O17087 · UniProt O61711
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