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Crystal structure of human IKK1
Analyse Crystal structure of human IKK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EBZ
- Type
- protein
- Length
- 7,860 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inhibitor of nuclear factor kappa-B kinase subunit alpha
- EC
- 2.7.11.10
- UniProt
- O15111
- Ligands
- 5LS, PDX, 5TL, 5TJ, 5TM, Z4K, 5TK, 5TH, GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Inhibitor of nuclear factor kappa-B kinase subunit alpha (EC 2.7.11.10) | protein | 655 | 45% helix, 8% strand | O15111 |
Ligands and binding sites
- 5LS · 2,4-di-O-sulfo-alpha-D-glucopyranose · ligand · 28 copies · chains A, B, F, C, E, D, G, H, J, L, I, K
- PDX · 2,3-di-O-sulfo-alpha-D-glucopyranose · ligand · 24 copies · chains A, B, C, D, F, E, G, H, J, L, I, K
- 5TL · 2-azanyl-5-phenyl-3-(4-sulfamoylphenyl)benzamide · ligand · 12 copies · chains A, B, C, D, E, F, G, I, H, J, K, L
- 5TJ · [(2R,3R,4R,5R,6S)-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate · ligand · 8 copies · chains A, D, C, H, I
- 5TM · [(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate · ligand · 4 copies · chains B, C, G
- Z4K · 2-O-sulfo-alpha-D-glucopyranose · ligand · 4 copies · chains C
- 5TK · (2S,3R,4R,5S,6R)-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol · ligand · 4 copies · chains C
- 5TH · [(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate · ligand · 4 copies · chains A, G, I
- GLC · alpha-D-glucopyranose · sugar · 24 copies · chains A, B, C, D, F, E, G, H, J, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.86 | 0.88 | 133 | empty |
| 2 | 890 | 0.85 | 0.87 | 102 | 5TL |
| 3 | 910 | 0.85 | 0.86 | 91 | 5TL |
| 4 | 693 | 0.84 | 0.88 | 93 | 5TL |
| 5 | 826 | 0.83 | 0.85 | 82 | empty |
Interfaces
19 interfaces between chains.
- A–B · 1827 Ų buried · 30 hydrogen bonds · protein-protein
- K–L · 1816 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1810 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1809 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1808 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5EBZ · Crystal structure of human IKK1 · 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 O15111
- Elsewhere: RCSB PDB 5EBZ · PDBe 5EBZ · UniProt O15111
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