MolNFT v1 · #162318 · protein

Crystal structure of ppep-1(W103F)

6R5A · Pro-pro endopeptidase: “Crystal structure of ppep-1(W103F)”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.78). MolNFT v1 #162318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6R5A
Type: protein
Length: 384 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pro-pro endopeptidase
EC: 3.4.24.89
UniProt: Q183R7
Ligands: ZN
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pro-pro endopeptidase (EC 3.4.24.89)	protein	192	55% helix, 8% strand	Q183R7

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

2 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	966	0.78	0.80	91	ZN, TRS
2	194	0.59	0.81	32	ZN, TRS

Interfaces

1 interface between chains.

A–B · 471 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6R5A · Crystal structure of PPEP-1(W103F) · the same entry in another collection · chain A against A, TM-score 1.00
Q183R7 · AlphaFold monomer V2.0 prediction for pro-pro endopeptidase (Q183R7) · 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 Q183R7
Elsewhere: RCSB PDB 6R5A · PDBe 6R5A · UniProt Q183R7

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