Research workbench
Crystal structure of chaetomium thermophilum NUP53 rrm (space group P3121)
Analyse Crystal structure of chaetomium thermophilum NUP53 rrm (space group P3121) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HB8
- Type
- protein
- Length
- 437 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin NUP53
- UniProt
- G0S156
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoporin NUP53 | protein | 109 | 29% helix, 23% strand | G0S156 |
| C | Nucleoporin NUP53 | protein | 110 | 29% helix, 23% strand | G0S156 |
| D | Nucleoporin NUP53 | protein | 109 | 28% helix, 23% strand | G0S156 |
Ligands and binding sites
- SIN · Succinic acid · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.74 | 0.77 | 123 | SIN, GOL |
Interfaces
6 interfaces between chains.
- A–C · 658 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HB8 · Crystal structure of Chaetomium thermophilum Nup53 RRM (space group P3121) · the same entry in another collection · chain B against B, TM-score 1.00
- G0S156 · AlphaFold monomer V2.0 prediction for nucleoporin NUP53 (G0S156) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 G0S156
- Elsewhere: RCSB PDB 5HB8 · PDBe 5HB8 · UniProt G0S156
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