MolNFT v1 · #94884 · protein
Structure of the C-terminal domain of NUP358
4I9Y · E3 sumo-protein ligase RANBP2: “Structure of the C-terminal domain of NUP358”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.75). MolNFT v1 #94884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4I9Y
- Type
- protein
- Length
- 1,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 sumo-protein ligase RANBP2
- UniProt
- P49792
- Ligands
- CL
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | E3 sumo-protein ligase RANBP2 | protein | 167 | 14% helix, 33% strand | P49792 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 21 copies · chains A, B, D, F, C, E
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.75 | 0.97 | 19 | TLA |
| 2 | 819 | 0.75 | 0.79 | 72 | GOL |
| 3 | 69 | 0.72 | 0.96 | 18 | TLA |
| 4 | 348 | 0.61 | 0.78 | 50 | GOL |
| 5 | 230 | 0.54 | 0.78 | 29 | empty |
Interfaces
8 interfaces between chains.
- E–F · 655 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 647 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 312 Ų buried · 1 hydrogen bond · protein-protein
- B–E · 267 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 263 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4I9Y · Structure of the C-terminal domain of Nup358 · 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 P49792
- Elsewhere: RCSB PDB 4I9Y · PDBe 4I9Y · UniProt P49792
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