Research workbench
Karyopherin nuclear state
Analyse Karyopherin nuclear state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICQ
- Type
- protein + RNA
- Length
- 2,346 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-T; GTP-binding nuclear protein GSP1/CNR1; RNA (62-mer)
- UniProt
- O94258, P32835
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Exportin-T | protein | 949 | 75% helix, 0% strand | O94258 |
| B | GTP-binding nuclear protein GSP1/CNR1 | protein | 167 | 25% helix, 26% strand | P32835 |
| D | RNA (62-mer) | rna | 62 | — | — |
| U | Exportin-T | protein | 943 | 73% helix, 0% strand | O94258 |
| C | GTP-binding nuclear protein GSP1/CNR1 | protein | 163 | 27% helix, 25% strand | P32835 |
| E | RNA (62-mer) | rna | 62 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains T, B, U, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.78 | 0.82 | 72 | empty |
| 2 | 1155 | 0.78 | 0.80 | 95 | empty |
| 3 | 725 | 0.78 | 0.82 | 64 | empty |
| 4 | 81 | 0.76 | 0.97 | 21 | empty |
| 5 | 678 | 0.72 | 0.80 | 66 | empty |
Interfaces
7 interfaces between chains.
- T–B · 1417 Ų buried · 12 hydrogen bonds · protein-protein
- U–C · 1293 Ų buried · 9 hydrogen bonds · protein-protein
- T–D · 1216 Ų buried · 24 hydrogen bonds · protein-nucleic
- U–E · 1132 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–D · 341 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3ICQ · Karyopherin nuclear state · the same entry in another collection · chain E against E, TM-score 1.00
- P32835 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein GSP1/CNR1 (P32835) · a predicted model of the same protein · chain B against A, TM-score 0.98
- O94258 · AlphaFold monomer V2.0 prediction for exportin-T (O94258) · a predicted model of the same protein · chain T against A, TM-score 0.97
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 O94258
- Every structure of UniProt P32835
- Elsewhere: RCSB PDB 3ICQ · PDBe 3ICQ · UniProt O94258 · UniProt P32835
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