Research workbench
Crystal structure of MDIA2 nes peptide in complex with CRM1-ran-RANBP1
Analyse Crystal structure of MDIA2 nes peptide in complex with CRM1-ran-RANBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UWP
- Type
- protein
- Length
- 1,344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein 1; Exportin-1…
- UniProt
- P62826, P41920, P30822
- Ligands
- GNP, MG
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 209 | 33% helix, 22% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 128 | 15% helix, 48% strand | P41920 |
| C | Exportin-1 | protein | 996 | 79% helix, 0% strand | P30822 |
| D | Protein diaphanous homolog 3 | protein | 11 | 73% helix, 0% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.86 | 0.88 | 124 | GOL |
| 2 | 171 | 0.65 | 0.86 | 31 | GNP, MG |
| 3 | 422 | 0.59 | 0.75 | 40 | empty |
| 4 | 127 | 0.58 | 0.84 | 17 | empty |
| 5 | 246 | 0.53 | 0.76 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2112 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1966 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 655 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5UWP · Crystal Structure of mDia2 NES Peptide in complex with CRM1-Ran-RanBP1 · the same entry in another collection · chain A against A, TM-score 1.00
- P30822 · AlphaFold monomer V2.0 prediction for exportin-1 (P30822) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P62826
- Every structure of UniProt P41920
- Every structure of UniProt P30822
- Elsewhere: RCSB PDB 5UWP · PDBe 5UWP · UniProt P62826 · UniProt P41920 · UniProt P30822
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