MolNFT v1 · #15788 · protein

I-kappa-B-ALPHA/NF-kappa-B complex

1NFI · Nf-kappa-B P65: “I-kappa-B-ALPHA/NF-kappa-B complex”. X-ray diffraction, 18 pockets (best druggability 0.66). MolNFT v1 #15788 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NFI
Type: protein
Length: 1,236 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nf-kappa-B P65; Nf-kappa-B P50; I-kappa-B-alpha
UniProt: Q04206, P19838, P25963
Pockets: 18 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 18% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nf-kappa-B P65	protein	295	8% helix, 35% strand	Q04206
B, D	Nf-kappa-B P50	protein	107	3% helix, 45% strand	P19838
C	Nf-kappa-B P65	protein	301	10% helix, 34% strand	Q04206
E, F	I-kappa-B-alpha	protein	213	50% helix, 0% strand	P25963

Pockets

18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	559	0.66	0.77	51	empty
2	528	0.65	0.77	52	empty
3	344	0.63	0.79	42	empty
4	297	0.61	0.79	36	empty
5	270	0.53	0.75	29	empty

Interfaces

8 interfaces between chains.

C–E · 1628 Å² buried · 22 hydrogen bonds · protein-protein
A–F · 1458 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 715 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 715 Å² buried · 11 hydrogen bonds · protein-protein
B–F · 615 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1NFI · I-kappa-B-ALPHA/NF-kappa-B complex · the same entry in another collection · chain F against F, TM-score 1.00
P25963 · AlphaFold monomer V2.0 prediction for nf-kappa-B inhibitor alpha (P25963) · a predicted model of the same protein · chain E against A, TM-score 0.99
P19838 · AlphaFold monomer V2.0 prediction for nuclear factor nf-kappa-B P105 subunit (P19838) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q04206 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04206) · a predicted model of the same protein · chain A against A, TM-score 0.64

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 Q04206
Every structure of UniProt P19838
Every structure of UniProt P25963
Elsewhere: RCSB PDB 1NFI · PDBe 1NFI · UniProt Q04206 · UniProt P19838 · UniProt P25963

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