MolNFT v1 · #82664 · protein

Crystal structure of T7-tagged optineurin lir-fused human LC3B_2-119

3VTW · Optineurin, microtubule-associated proteins 1A/1B light…: “Crystal structure of T7-tagged optineurin lir-fused human LC3B_2-119”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.61). MolNFT v1 #82664 on GenesisL1…

PDB: 3VTW
Type: protein
Length: 375 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Optineurin, microtubule-associated proteins 1A/1B light chain 3B
UniProt: Q96CV9, Q9GZQ8
Ligands: SO4
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Optineurin, microtubule-associated proteins 1A/1B light chain 3B	protein	125	30% helix, 22% strand	Q96CV9, Q9GZQ8

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C

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

Pockets

5 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	185	0.61	0.83	34	SO4
2	308	0.55	0.76	50	empty
3	102	0.39	0.76	23	empty
4	52	0.34	0.78	14	empty
5	65	0.29	0.73	16	empty

Interfaces

2 interfaces between chains.

A–B · 528 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 512 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3VTW · Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 · the same entry in another collection · chain A against A, TM-score 1.00
Q9GZQ8 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain A against A, TM-score 0.88
Q96CV9 · AlphaFold monomer V2.0 prediction for optineurin (Q96CV9) · a predicted model of the same protein · chain A against A, TM-score 0.21

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 Q96CV9
Every structure of UniProt Q9GZQ8
Elsewhere: RCSB PDB 3VTW · PDBe 3VTW · UniProt Q96CV9 · UniProt Q9GZQ8

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