MolNFT v1 · #51336 · protein

Nemo CC2-lz domain - 1D5 darpin complex

2V4H · Nf-kappa-B essential modulator: “Nemo CC2-lz domain - 1D5 darpin complex”. X-ray diffraction, 4 pockets (best druggability 0.47). MolNFT v1 #51336 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2V4H
Type: protein
Length: 442 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nf-kappa-B essential modulator; 1D5 darpin
UniProt: O88522
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nf-kappa-B essential modulator	protein	98	83% helix, 0% strand	O88522
B	Nf-kappa-B essential modulator	protein	91	95% helix, 0% strand	O88522
C	1D5 darpin	protein	125	51% helix, 2% strand	—
D	1D5 darpin	protein	128	54% helix, 0% strand	—

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.47	0.78	23	empty
2	104	0.44	0.78	17	empty
3	139	0.43	0.76	24	empty
4	83	0.38	0.77	16	empty

Interfaces

5 interfaces between chains.

A–B · 2444 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 543 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 534 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 296 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 277 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2V4H · NEMO CC2-LZ domain - 1D5 DARPin complex · the same entry in another collection · chain A against A, 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 0.82

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 O88522
Elsewhere: RCSB PDB 2V4H · PDBe 2V4H · UniProt O88522

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