MolNFT v1 · #163053 · protein

Sidd, deampylase from legionella pneumophila

6RRE · Adenosine monophosphate-protein hydrolase sidd: “Sidd, deampylase from legionella pneumophila”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.76). MolNFT v1 #163053 on GenesisL1: 3D structure, binding sites and…

PDB: 6RRE
Type: protein
Length: 2,497 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenosine monophosphate-protein hydrolase sidd
UniProt: Q6RCR2
Ligands: MG
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenosine monophosphate-protein hydrolase sidd	protein	411	43% helix, 22% strand	Q6RCR2
B	Adenosine monophosphate-protein hydrolase sidd	protein	422	41% helix, 22% strand	Q6RCR2
C	Adenosine monophosphate-protein hydrolase sidd	protein	421	42% helix, 23% strand	Q6RCR2
D	Adenosine monophosphate-protein hydrolase sidd	protein	427	42% helix, 22% strand	Q6RCR2
E	Adenosine monophosphate-protein hydrolase sidd	protein	409	43% helix, 22% strand	Q6RCR2
F	Adenosine monophosphate-protein hydrolase sidd	protein	407	43% helix, 21% strand	Q6RCR2

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains B, C, D, F

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.76	0.94	25	empty
2	873	0.75	0.79	68	empty
3	1041	0.74	0.77	68	empty
4	1098	0.74	0.77	98	empty
5	683	0.73	0.79	79	empty

Interfaces

6 interfaces between chains.

A–C · 879 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 870 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 669 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 581 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 417 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6RRE · SidD, deAMPylase from Legionella pneumophila · 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 Q6RCR2
Elsewhere: RCSB PDB 6RRE · PDBe 6RRE · UniProt Q6RCR2

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