Research workbench
Crystal structure of ran-gppnhp-RANBP1-rangap complex
Analyse Crystal structure of ran-gppnhp-RANBP1-rangap complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K5D
- Type
- protein
- Length
- 2,784 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein; Ran GTPase…
- UniProt
- P62826, P43487, P41391
- Ligands
- GNP, MG
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | GTP-binding nuclear protein ran | protein | 206 | 29% helix, 23% strand | P62826 |
| B, E, H, K | Ran-specific GTPase-activating protein | protein | 146 | 14% helix, 37% strand | P43487 |
| C, F, I, L | Ran GTPase activating protein 1 | protein | 344 | 43% helix, 11% strand | P41391 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, C, D, F, G, I, J
- MG · Magnesium ion · metal · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.70 | 0.82 | 52 | MG, GNP |
| 2 | 371 | 0.69 | 0.82 | 55 | MG, GNP |
| 3 | 380 | 0.69 | 0.82 | 53 | MG, GNP |
| 4 | 244 | 0.69 | 0.84 | 38 | empty |
| 5 | 379 | 0.68 | 0.81 | 52 | MG, GNP |
Interfaces
13 interfaces between chains.
- J–K · 2792 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2778 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2771 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2768 Ų buried · 37 hydrogen bonds · protein-protein
- J–L · 1344 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1K5D · Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex · the same entry in another collection · chain L against L, 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 P43487
- Every structure of UniProt P41391
- Elsewhere: RCSB PDB 1K5D · PDBe 1K5D · UniProt P62826 · UniProt P43487 · UniProt P41391
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