Research workbench
Yeast CRM1E (apo) in complex with ran-RANBP1
Analyse Yeast CRM1E (apo) in complex with ran-RANBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DBG
- Type
- protein
- Length
- 1,324 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; YRB1 isoform 1; CRM1 isoform 1
- UniProt
- P62826, A0A6A5PZB5, A0A6A5PZI8
- Ligands
- GTP, MG, CL
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 209 | 30% helix, 22% strand | P62826 |
| B | YRB1 isoform 1 | protein | 119 | 16% helix, 50% strand | A0A6A5PZB5 |
| C | CRM1 isoform 1 | protein | 996 | 79% helix, 0% strand | A0A6A5PZI8 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 12 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains C
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.87 | 0.88 | 147 | MG, GTP, CL |
| 2 | 709 | 0.67 | 0.76 | 73 | empty |
| 3 | 260 | 0.61 | 0.80 | 29 | CL |
| 4 | 83 | 0.54 | 0.85 | 17 | empty |
| 5 | 125 | 0.49 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1975 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1961 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7DBG · Yeast CRM1e (apo) in complex with Ran-RanBP1 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A6A5PZB5
- Every structure of UniProt A0A6A5PZI8
- Elsewhere: RCSB PDB 7DBG · PDBe 7DBG · UniProt P62826 · UniProt A0A6A5PZB5 · UniProt A0A6A5PZI8
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