MolNFT v1 · #79657 · protein

Regulatory czb domain of dgcz

3T9O · Diguanylate cyclase dgcz: “Regulatory czb domain of dgcz”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.59). MolNFT v1 #79657 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3T9O
Type: protein
Length: 228 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diguanylate cyclase dgcz
EC: 2.7.7.65
UniProt: P31129
Ligands: ZN
Pockets: 1 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diguanylate cyclase dgcz (EC 2.7.7.65)	protein	108	82% helix, 0% strand	P31129
B	Diguanylate cyclase dgcz (EC 2.7.7.65)	protein	120	78% helix, 0% strand	P31129

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.59	0.80	25	empty

Interfaces

1 interface between chains.

A–B · 1361 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3T9O · Regulatory CZB domain of DgcZ · the same entry in another collection · chain A against A, TM-score 1.00
P31129 · AlphaFold monomer V2.0 prediction for diguanylate cyclase dgcz (P31129) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P31129
Elsewhere: RCSB PDB 3T9O · PDBe 3T9O · UniProt P31129

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