MolNFT v1 · #139123 · protein

Crystal structure of a hydrolase encoded by LIN2189 from listeria innocua

5X5M · LIN2189 protein: “Crystal structure of a hydrolase encoded by LIN2189 from listeria innocua”. X-ray diffraction, 1 ligand (7YU), 4 pockets (best druggability 0.62). MolNFT v1 #139123 on GenesisL1: 3D structure, binding sites and…

PDB: 5X5M
Type: protein
Length: 410 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LIN2189 protein
UniProt: Q929T5
Ligands: 7YU
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	LIN2189 protein	protein	205	33% helix, 31% strand	Q929T5

Ligands and binding sites

7YU · (+)-Yatakemycin · ligand · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B

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

Pockets

4 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	336	0.62	0.78	45	DMS, 7YU
2	340	0.62	0.78	43	DMS, 7YU
3	336	0.55	0.75	44	empty
4	87	0.41	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 336 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5X5M · Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua · the same entry in another collection · chain A against A, TM-score 1.00

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 Q929T5
Elsewhere: RCSB PDB 5X5M · PDBe 5X5M · UniProt Q929T5

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