MolNFT v1 · #106302 · protein

Characterization of an essential diadenylate cyclase

4RV7: “Characterization of an essential diadenylate cyclase”. X-ray diffraction, 2 ligands (ATP, MG), 11 pockets (best druggability 0.55). MolNFT v1 #106302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RV7
Type: protein
Length: 633 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diadenylate cyclase
EC: 2.7.7.85
UniProt: Q8Y5E4
Ligands: ATP, MG
Pockets: 11 · best druggability 0.55

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diadenylate cyclase (EC 2.7.7.85)	protein	159	41% helix, 23% strand	Q8Y5E4
B	Diadenylate cyclase (EC 2.7.7.85)	protein	158	40% helix, 23% strand	Q8Y5E4
C	Diadenylate cyclase (EC 2.7.7.85)	protein	161	39% helix, 22% strand	Q8Y5E4
D	Diadenylate cyclase (EC 2.7.7.85)	protein	155	43% helix, 23% strand	Q8Y5E4

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, C, B, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
HEZ · Hexane-1,6-diol · additive · chains A

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

Pockets

11 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	263	0.55	0.77	44	ATP
2	161	0.52	0.79	30	ATP
3	121	0.48	0.79	15	ATP
4	65	0.37	0.78	16	empty
5	60	0.34	0.77	15	empty

Interfaces

4 interfaces between chains.

B–D · 684 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 684 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 652 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 54 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4RV7 · Characterization of an essential diadenylate cyclase · the same entry in another collection · chain D against D, TM-score 1.00
Q8Y5E4 · AlphaFold monomer V2.0 prediction for diadenylate cyclase (Q8Y5E4) · a predicted model of the same protein · chain B 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 Q8Y5E4
Elsewhere: RCSB PDB 4RV7 · PDBe 4RV7 · UniProt Q8Y5E4

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