MolNFT v1 · #120770 · protein
Crystal structure of chaetomium thermophilum NUP170 ntd-NUP53 complex
5HAX · Nucleoporin NUP170: “Crystal structure of chaetomium thermophilum NUP170 ntd-NUP53 complex”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.78). MolNFT v1 #120770 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HAX
- Type
- protein
- Length
- 712 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin NUP170; Nucleoporin NUP53
- UniProt
- G0S7B6, G0S156
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoporin NUP170 | protein | 698 | 30% helix, 28% strand | G0S7B6 |
| B | Nucleoporin NUP53 | protein | 14 | 29% helix, 29% strand | G0S156 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.78 | 0.80 | 57 | empty |
| 2 | 87 | 0.68 | 0.93 | 31 | empty |
| 3 | 236 | 0.52 | 0.76 | 39 | empty |
| 4 | 69 | 0.36 | 0.78 | 17 | empty |
| 5 | 81 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5HAX · Crystal structure of Chaetomium thermophilum Nup170 NTD-Nup53 complex · the same entry in another collection · chain A against A, TM-score 1.00
- G0S7B6 · AlphaFold monomer V2.0 prediction for nucleoporin NUP170 (G0S7B6) · a predicted model of the same protein · chain A against A, TM-score 1.00
- G0S156 · AlphaFold monomer V2.0 prediction for nucleoporin NUP53 (G0S156) · a predicted model of the same protein · chain B against A, TM-score 0.39
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 G0S7B6
- Every structure of UniProt G0S156
- Elsewhere: RCSB PDB 5HAX · PDBe 5HAX · UniProt G0S7B6 · UniProt G0S156
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