MolNFT v1 · #152522 · protein

Crystal structure of substrate-bound S9 peptidase (S514A mutant) from deinococcus radiodurans

6IKG · Acyl-peptide hydrolase, putative: “Crystal structure of substrate-bound S9 peptidase (S514A mutant) from deinococcus radiodurans”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #152522 on GenesisL1: 3D structure…

PDB: 6IKG
Type: protein
Length: 2,571 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-peptide hydrolase, putative; Met-ala-ala
UniProt: Q9RXY9
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Acyl-peptide hydrolase, putative	protein	644	18% helix, 35% strand	Q9RXY9
B	Acyl-peptide hydrolase, putative	protein	640	19% helix, 36% strand	Q9RXY9
C	Acyl-peptide hydrolase, putative	protein	641	19% helix, 36% strand	Q9RXY9
D	Acyl-peptide hydrolase, putative	protein	640	19% helix, 35% strand	Q9RXY9
E, F	Met-ala-ala	protein	3	0% helix, 33% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1027	0.79	0.81	101	empty
2	988	0.78	0.80	102	empty
3	517	0.76	0.84	70	empty
4	594	0.75	0.82	42	empty
5	472	0.75	0.84	35	empty

Interfaces

6 interfaces between chains.

A–B · 2650 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 2641 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 706 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 680 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 319 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6IKG · Crystal structure of substrate-bound S9 peptidase (S514A mutant) from Deinococcus… · 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 6IKG · PDBe 6IKG · UniProt Q9RXY9

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