MolNFT v1 · #141203 · protein

Crystal structure of S9 peptidase mutant (S514A) from deinococcus radiodurans R1

5YZO · Acyl-peptide hydrolase, putative: “Crystal structure of S9 peptidase mutant (S514A) from deinococcus radiodurans R1”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #141203 on GenesisL1: 3D structure, binding…

PDB: 5YZO
Type: protein
Length: 2,579 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-peptide hydrolase, putative
UniProt: Q9RXY9
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-peptide hydrolase, putative	protein	649	18% helix, 36% strand	Q9RXY9
B	Acyl-peptide hydrolase, putative	protein	644	19% helix, 37% strand	Q9RXY9
C, D	Acyl-peptide hydrolase, putative	protein	643	19% helix, 37% strand	Q9RXY9

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.78	0.80	115	DMS, GOL
2	703	0.76	0.81	71	DMS
3	556	0.75	0.83	41	empty
4	593	0.75	0.82	46	empty
5	715	0.75	0.81	79	DMS, GOL

Interfaces

4 interfaces between chains.

A–D · 2644 Å² buried · 47 hydrogen bonds · protein-protein
B–C · 2639 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 735 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 725 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5YZO · Crystal structure of S9 peptidase mutant (S514A) from Deinococcus radiodurans R1 · 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 Q9RXY9
Elsewhere: RCSB PDB 5YZO · PDBe 5YZO · UniProt Q9RXY9

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