MolNFT v1 · #161239 · protein
Crystal structure of rangtp-PDR6-EIF5A export complex
6Q84 · Importin beta-like protein KAP122: “Crystal structure of rangtp-PDR6-EIF5A export complex”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #161239 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6Q84
- Type
- protein
- Length
- 2,641 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin beta-like protein KAP122; GTP-binding nuclear protein ran; Eukaryotic…
- UniProt
- P32767, P62826, P23301
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 62% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin beta-like protein KAP122 | protein | 1019 | 72% helix, 0% strand | P32767 |
| B, E | GTP-binding nuclear protein ran | protein | 171 | 26% helix, 27% strand | P62826 |
| C | Eukaryotic translation initiation factor 5A-1 | protein | 137 | 12% helix, 56% strand | P23301 |
| D | Importin beta-like protein KAP122 | protein | 1017 | 71% helix, 0% strand | P32767 |
| F | Eukaryotic translation initiation factor 5A-1 | protein | 126 | 13% helix, 55% strand | P23301 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.85 | 0.86 | 103 | GTP, MG |
| 2 | 1137 | 0.84 | 0.85 | 108 | GTP, MG |
| 3 | 622 | 0.77 | 0.83 | 72 | empty |
| 4 | 582 | 0.77 | 0.83 | 65 | empty |
| 5 | 838 | 0.71 | 0.76 | 76 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1887 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1051 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1005 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 576 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6Q84 · Crystal structure of RanGTP-Pdr6-eIF5A export complex · the same entry in another collection · chain F against F, TM-score 1.00
- P23301 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 5A-1… · a predicted model of the same protein · chain F against A, TM-score 0.96
- P32767 · AlphaFold monomer V2.0 prediction for importin beta-like protein KAP122 (P32767) · a predicted model of the same protein · chain D against A, TM-score 0.81
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 P32767
- Every structure of UniProt P62826
- Every structure of UniProt P23301
- Elsewhere: RCSB PDB 6Q84 · PDBe 6Q84 · UniProt P32767 · UniProt P62826 · UniProt P23301
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