MolNFT v1 · #179117 · protein

Crystal structure of an essential ribosomal processing protease prp from S. aureus in complex with a substrate peptide

7JVS · Ribosomal-processing cysteine protease prp: “Crystal structure of an essential ribosomal processing protease prp from S. aureus in complex with a…”. X-ray diffraction, 2 ligands (CA, NI), 1 pocket (best druggability 0.47). MolNFT v1…

PDB: 7JVS
Type: protein
Length: 223 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal-processing cysteine protease prp; L27 ribosomal peptide
UniProt: W8U5D2
Ligands: CA, NI
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	Ribosomal-processing cysteine protease prp	protein	106	38% helix, 27% strand	W8U5D2
C	L27 ribosomal peptide	protein	11	0% helix, 0% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B, D
NI · Nickel (II) ion · metal · chains D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.47	0.78	17	empty

Interfaces

3 interfaces between chains.

B–D · 902 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 652 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 251 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7JVS · Crystal Structure of an Essential Ribosomal Processing Protease Prp from S. aureus in… · the same entry in another collection · chain B against B, 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 W8U5D2
Elsewhere: RCSB PDB 7JVS · PDBe 7JVS · UniProt W8U5D2

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