MolNFT v1 · #17588 · protein
Crystal structure of an IKBBETA/NF-kb P65 homodimer complex
1OY3 · Transcription factor P65: “Crystal structure of an IKBBETA/NF-kb P65 homodimer complex”. X-ray diffraction, 4 pockets (best druggability 0.69). MolNFT v1 #17588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1OY3
- Type
- protein
- Length
- 467 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor P65; Transcription factor inhibitor I-kappa-B-beta
- UniProt
- Q04207, Q60778
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Transcription factor P65 | protein | 135 | 18% helix, 35% strand | Q04207 |
| B | Transcription factor P65 | protein | 112 | 3% helix, 43% strand | Q04207 |
| D | Transcription factor inhibitor I-kappa-B-beta | protein | 220 | 47% helix, 0% strand | Q60778 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.69 | 0.75 | 81 | empty |
| 2 | 235 | 0.59 | 0.80 | 33 | empty |
| 3 | 73 | 0.41 | 0.79 | 13 | empty |
| 4 | 51 | 0.24 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1242 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 702 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 506 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1OY3 · Crystal structure of an IKBBETA/NF-kb P65 homodimer complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q60778 · AlphaFold monomer V2.0 prediction for nf-kappa-B inhibitor beta (Q60778) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q04207
- Every structure of UniProt Q60778
- Elsewhere: RCSB PDB 1OY3 · PDBe 1OY3 · UniProt Q04207 · UniProt Q60778
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