Research workbench
Crystal structure of a fragment of nuclear factor related to kappa-B- binding protein (residues 370-495) (nfrkb) from homo sapiens at 2.18 a resolution
Analyse Crystal structure of a fragment of nuclear factor related to kappa-B- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U21
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear factor related to kappa-B-binding protein
- UniProt
- Q6P4R8
- Ligands
- NA
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear factor related to kappa-B-binding protein | protein | 109 | 50% helix, 10% strand | Q6P4R8 |
| B | Nuclear factor related to kappa-B-binding protein | protein | 108 | 55% helix, 9% strand | Q6P4R8 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.42 | 0.76 | 15 | empty |
| 2 | 79 | 0.38 | 0.78 | 18 | empty |
| 3 | 56 | 0.36 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 675 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (methylation, engineered).
Compared structures
- 3U21 · Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P4R8 · AlphaFold monomer V2.0 prediction for nuclear factor related to kappa-B-binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q6P4R8
- Elsewhere: RCSB PDB 3U21 · PDBe 3U21 · UniProt Q6P4R8
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