MolNFT v1 · #148125 · protein

Crystal structure of rhodesain in complex with a macrolactam inhibitor

6EXO · Cysteine protease: “Crystal structure of rhodesain in complex with a macrolactam inhibitor”. X-ray diffraction, 1 ligand (C3E), 6 pockets (best druggability 0.78). MolNFT v1 #148125 on GenesisL1: 3D structure, binding sites and…

PDB: 6EXO
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cysteine protease
UniProt: Q95PM0
Ligands: C3E
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cysteine protease	protein	215	27% helix, 23% strand	Q95PM0

Ligands and binding sites

C3E · (3~{S},14~{E})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 23 copies · chains A, B

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

Pockets

6 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	473	0.78	0.86	47	EDO
2	72	0.32	0.75	18	EDO
3	64	0.32	0.76	17	C3E
4	74	0.32	0.74	18	empty
5	73	0.31	0.74	23	EDO

Interfaces

1 interface between chains.

A–B · 506 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).

Compared structures

6EXO · Crystal Structure of Rhodesain in complex with a Macrolactam Inhibitor · 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 Q95PM0
Elsewhere: RCSB PDB 6EXO · PDBe 6EXO · UniProt Q95PM0

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