MolNFT v1 · #142322 · protein

The crystal structure of LPG2622_E64 complex

6A0Q: “The crystal structure of LPG2622_E64 complex”. X-ray diffraction, 1 ligand (E64), 8 pockets (best druggability 0.57). MolNFT v1 #142322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6A0Q
Type: protein
Length: 639 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LPG2622
UniProt: Q5ZS97
Ligands: E64
Pockets: 8 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LPG2622	protein	324	30% helix, 29% strand	Q5ZS97
B	LPG2622	protein	315	31% helix, 29% strand	Q5ZS97

Ligands and binding sites

E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · chains B

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

Pockets

8 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	74	0.57	0.87	22	E64
2	52	0.49	0.87	14	empty
3	58	0.45	0.83	18	empty
4	98	0.39	0.76	18	empty
5	91	0.35	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 27 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6A0Q · The crystal structure of Lpg2622_E64 complex · 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 Q5ZS97
Elsewhere: RCSB PDB 6A0Q · PDBe 6A0Q · UniProt Q5ZS97

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