MolNFT v1 · #56947 · protein

Nemo cozi domain incomplex with diubiquitin in P212121 space group

2ZVN · Ubc protein: “Nemo cozi domain incomplex with diubiquitin in P212121 space group”. X-ray diffraction, 11 pockets (best druggability 0.65). MolNFT v1 #56947 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ZVN
Type: protein
Length: 931 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubc protein; Nf-kappa-B essential modulator
UniProt: Q96C32, O88522
Pockets: 11 · best druggability 0.65

Structure

x-ray diffraction · 6 distinct chains · 47% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubc protein	protein	148	18% helix, 31% strand	Q96C32
G, E	Ubc protein	protein	146	24% helix, 31% strand	Q96C32
B	Nf-kappa-B essential modulator	protein	85	93% helix, 0% strand	O88522
D	Nf-kappa-B essential modulator	protein	85	93% helix, 0% strand	O88522
C	Ubc protein	protein	149	21% helix, 32% strand	Q96C32
F, H	Nf-kappa-B essential modulator	protein	86	95% helix, 0% strand	O88522

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.65	0.75	80	empty
2	438	0.63	0.77	57	empty
3	209	0.47	0.74	31	empty
4	66	0.46	0.82	14	empty
5	215	0.45	0.73	34	empty

Interfaces

13 interfaces between chains.

B–D · 2375 Å² buried · 10 hydrogen bonds · protein-protein
F–H · 2370 Å² buried · 10 hydrogen bonds · protein-protein
C–H · 688 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 676 Å² buried · 6 hydrogen bonds · protein-protein
G–B · 630 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2ZVN · NEMO CoZi domain incomplex with diubiquitin in P212121 space group · the same entry in another collection · chain H against H, TM-score 1.00
O88522 · AlphaFold monomer V2.0 prediction for nf-kappa-B essential modulator (O88522) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 Q96C32
Every structure of UniProt O88522
Elsewhere: RCSB PDB 2ZVN · PDBe 2ZVN · UniProt Q96C32 · UniProt O88522

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