Research workbench
Crystal structures of the HMTR4-NRDE2 complex
Analyse Crystal structures of the HMTR4-NRDE2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IEH
- Type
- protein
- Length
- 1,014 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome RNA helicase MTR4; Protein NRDE2 homolog
- EC
- 3.6.4.13
- UniProt
- P42285, Q9H7Z3
- Ligands
- ATP, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Exosome RNA helicase MTR4 (EC 3.6.4.13) | protein | 929 | 48% helix, 17% strand | P42285 |
| A | Protein NRDE2 homolog | protein | 85 | 15% helix, 9% strand | Q9H7Z3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.79 | 0.81 | 102 | ATP |
| 2 | 661 | 0.68 | 0.77 | 57 | empty |
| 3 | 196 | 0.54 | 0.78 | 24 | empty |
| 4 | 241 | 0.51 | 0.75 | 39 | empty |
| 5 | 139 | 0.51 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 3963 Ų buried · 59 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6IEH · Crystal structures of the hMTR4-NRDE2 complex · the same entry in another collection · chain B against B, TM-score 1.00
- P42285 · AlphaFold monomer V2.0 prediction for exosome RNA helicase MTR4 (P42285) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9H7Z3 · AlphaFold monomer V2.0 prediction for nuclear exosome regulator NRDE2 (Q9H7Z3) · a predicted model of the same protein · chain A against A, TM-score 0.41
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 P42285
- Every structure of UniProt Q9H7Z3
- Elsewhere: RCSB PDB 6IEH · PDBe 6IEH · UniProt P42285 · UniProt Q9H7Z3
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