Research workbench
Crystal structure of DMNXF2 NTF2-like domain in complex with NXT1/P15
Analyse Crystal structure of DMNXF2 NTF2-like domain in complex with NXT1/P15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MRK
- Type
- protein
- Length
- 629 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear RNA export factor 2; NTF2-related export protein
- UniProt
- Q9VV73, Q9V3H8
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear RNA export factor 2 | protein | 183 | 33% helix, 34% strand | Q9VV73 |
| U | NTF2-related export protein | protein | 132 | 30% helix, 45% strand | Q9V3H8 |
| B | Nuclear RNA export factor 2 | protein | 188 | 29% helix, 37% strand | Q9VV73 |
| V | NTF2-related export protein | protein | 126 | 30% helix, 45% strand | Q9V3H8 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.80 | 0.82 | 72 | empty |
| 2 | 233 | 0.66 | 0.84 | 34 | empty |
| 3 | 143 | 0.53 | 0.81 | 27 | empty |
| 4 | 125 | 0.47 | 0.79 | 23 | empty |
| 5 | 93 | 0.46 | 0.80 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–U · 2053 Ų buried · 34 hydrogen bonds · protein-protein
- B–V · 1920 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 834 Ų buried · 11 hydrogen bonds · protein-protein
- U–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MRK · Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15 · the same entry in another collection · chain V against V, TM-score 1.00
- Q9V3H8 · AlphaFold monomer V2.0 prediction for NTF2-related export protein (Q9V3H8) · a predicted model of the same protein · chain V against A, TM-score 0.98
- Q9VV73 · AlphaFold monomer V2.0 prediction for nuclear RNA export factor 2 (Q9VV73) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9VV73
- Every structure of UniProt Q9V3H8
- Elsewhere: RCSB PDB 6MRK · PDBe 6MRK · UniProt Q9VV73 · UniProt Q9V3H8
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