MolNFT v1 · #70779 · protein

Structure of ulilysin mutant M290L

3LUM: “Structure of ulilysin mutant M290L”. X-ray diffraction, 2 ligands (CA, ZN), 7 pockets (best druggability 0.86). MolNFT v1 #70779 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3LUM
Type: protein
Length: 1,056 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ulilysin
EC: 3.4.24.-
UniProt: Q8TL28
Ligands: CA, ZN
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ulilysin (EC 3.4.24.-)	protein	264	26% helix, 18% strand	Q8TL28

Ligands and binding sites

CA · Calcium ion · metal · 11 copies · chains A, C, B, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 9 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.86	0.87	65	CA, ZN
2	568	0.70	0.79	44	GOL
3	511	0.67	0.78	40	empty
4	117	0.42	0.76	25	empty
5	112	0.36	0.73	19	empty

Interfaces

4 interfaces between chains.

A–C · 1240 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 491 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 477 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 73 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3LUM · Structure of ulilysin mutant M290L · the same entry in another collection · chain A against A, TM-score 1.00
Q8TL28 · AlphaFold monomer V2.0 prediction for ulilysin (Q8TL28) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8TL28
Elsewhere: RCSB PDB 3LUM · PDBe 3LUM · UniProt Q8TL28

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