MolNFT v1 · #171577 · protein
Crystal structure of a TSEN15-34 heterodimer.
6Z9U · TRNA-splicing endonuclease subunit SEN34: “Crystal structure of a TSEN15-34 heterodimer.”. X-ray diffraction, 6 pockets (best druggability 0.50). MolNFT v1 #171577 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z9U
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-splicing endonuclease subunit SEN34; TRNA-splicing endonuclease subunit SEN15
- EC
- 4.6.1.16
- UniProt
- Q9BSV6, Q8WW01
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-splicing endonuclease subunit SEN34 (EC 4.6.1.16) | protein | 88 | 18% helix, 40% strand | Q9BSV6 |
| B | TRNA-splicing endonuclease subunit SEN15 | protein | 127 | 35% helix, 30% strand | Q8WW01 |
| C | TRNA-splicing endonuclease subunit SEN34 (EC 4.6.1.16) | protein | 95 | 26% helix, 31% strand | Q9BSV6 |
| D | TRNA-splicing endonuclease subunit SEN15 | protein | 134 | 34% helix, 31% strand | Q8WW01 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.50 | 0.83 | 18 | empty |
| 2 | 103 | 0.44 | 0.78 | 19 | empty |
| 3 | 56 | 0.34 | 0.78 | 18 | empty |
| 4 | 59 | 0.32 | 0.76 | 14 | empty |
| 5 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2023 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1663 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1403 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 170 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 107 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Z9U · Crystal structure of a TSEN15-34 heterodimer. · the same entry in another collection · chain D against D, TM-score 1.00
- Q8WW01 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease subunit SEN15 (Q8WW01) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9BSV6 · AlphaFold monomer V2.0 prediction for tRNA-splicing endonuclease subunit SEN34 (Q9BSV6) · a predicted model of the same protein · chain A against A, TM-score 0.56
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 Q9BSV6
- Every structure of UniProt Q8WW01
- Elsewhere: RCSB PDB 6Z9U · PDBe 6Z9U · UniProt Q9BSV6 · UniProt Q8WW01
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