MolNFT v1 · #12070 · protein
Crystal structure of ran-GDP-alfx-RANBP1-rangap complex
1K5G · GTP-binding nuclear protein ran: “Crystal structure of ran-GDP-alfx-RANBP1-rangap complex”. X-ray diffraction, 3 ligands (GDP, AF3, MG), 20 pockets (best druggability 0.68). MolNFT v1 #12070 on GenesisL1: 3D structure, binding sites…
- PDB
- 1K5G
- 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
- GDP, AF3, MG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | GTP-binding nuclear protein ran | protein | 206 | 27% helix, 23% strand | P62826 |
| B, E, H, K | Ran-specific GTPase-activating protein | protein | 146 | 13% helix, 37% strand | P43487 |
| C, F, I, L | Ran GTPase activating protein 1 | protein | 344 | 42% helix, 12% strand | P41391 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, C, D, F, G, I, J, L
- AF3 · Aluminum fluoride · ligand · 4 copies · chains A, D, G, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.68 | 0.82 | 48 | MG, GDP, AF3 |
| 2 | 358 | 0.68 | 0.81 | 52 | MG, GDP, AF3 |
| 3 | 369 | 0.67 | 0.81 | 51 | MG, GDP, AF3 |
| 4 | 358 | 0.66 | 0.81 | 53 | MG, GDP, AF3 |
| 5 | 235 | 0.63 | 0.82 | 40 | empty |
Interfaces
13 interfaces between chains.
- J–K · 2848 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2841 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 2841 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2840 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1394 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1K5G · Crystal structure of Ran-GDP-AlFx-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 1K5G · PDBe 1K5G · UniProt P62826 · UniProt P43487 · UniProt P41391
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