MolNFT v1 · #156381 · protein

MUL1-ring domain

6M2D · Mitochondrial ubiquitin ligase activator of nfkb 1: “MUL1-ring domain”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.69). MolNFT v1 #156381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6M2D
Type: protein
Length: 338 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial ubiquitin ligase activator of nfkb 1
EC: 2.3.2.27
UniProt: Q969V5
Ligands: ZN, SO4
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Mitochondrial ubiquitin ligase activator of nfkb 1 (EC 2.3.2.27)	protein	57	18% helix, 21% strand	Q969V5
D, F	Mitochondrial ubiquitin ligase activator of nfkb 1 (EC 2.3.2.27)	protein	55	11% helix, 24% strand	Q969V5

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	774	0.69	0.76	72	SO4
2	170	0.47	0.76	17	empty
3	132	0.46	0.77	22	empty
4	106	0.44	0.78	20	empty
5	97	0.38	0.75	15	empty

Interfaces

9 interfaces between chains.

B–D · 632 Å² buried · 10 hydrogen bonds · protein-protein
C–F · 584 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 497 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 448 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 432 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6M2D · MUL1-RING domain · the same entry in another collection · chain F against F, TM-score 1.00
Q969V5 · AlphaFold monomer V2.0 prediction for mitochondrial ubiquitin ligase activator of nfkb 1… · a predicted model of the same protein · chain D against A, TM-score 0.92

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 Q969V5
Elsewhere: RCSB PDB 6M2D · PDBe 6M2D · UniProt Q969V5

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